Starting phenix.real_space_refine on Sun Aug 24 15:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0o_35907/08_2025/8j0o_35907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0o_35907/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j0o_35907/08_2025/8j0o_35907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0o_35907/08_2025/8j0o_35907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j0o_35907/08_2025/8j0o_35907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0o_35907/08_2025/8j0o_35907.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.42, per 1000 atoms: 0.21 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: 1.51 Conformation dependent library (CDL) restraints added in 802.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.48 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: 3.21 Time building geometry restraints manager: 1.93 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: 3.850 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- 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 21465 Z= 0.956 Angle : 0.973 49.189 29095 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 : 12.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG B 224 TYR 0.025 0.001 TYR E 91 PHE 0.042 0.001 PHE A 581 TRP 0.034 0.001 TRP H 164 HIS 0.014 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.01375 (21456) covalent geometry : angle 0.96977 (29068) hydrogen bonds : bond 0.15931 ( 972) hydrogen bonds : angle 6.34063 ( 2847) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 1.34171 ( 18) link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 4.27533 ( 9) *********************** 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 : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.5469 (pt) REVERT: C 222 TRP cc_start: 0.6412 (t60) cc_final: 0.6143 (t60) REVERT: F 90 ILE cc_start: 0.6958 (mt) cc_final: 0.6750 (mp) REVERT: G 47 ILE cc_start: 0.6516 (mt) cc_final: 0.5989 (mt) REVERT: G 162 MET cc_start: 0.4922 (ptp) cc_final: 0.4594 (ttp) REVERT: H 7 THR cc_start: 0.5261 (p) cc_final: 0.5018 (p) outliers start: 9 outliers final: 0 residues processed: 540 average time/residue: 0.1565 time to fit residues: 123.8205 Evaluate side-chains 295 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 521 ASN 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 ** 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** C 53 GLN C 64 ASN C 200 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS D 51 GLN ** 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 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 K 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.099256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.081311 restraints weight = 82699.950| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 5.01 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3619 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 21465 Z= 0.169 Angle : 0.801 14.060 29095 Z= 0.387 Chirality : 0.046 0.257 3279 Planarity : 0.005 0.083 3679 Dihedral : 6.494 57.795 3028 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.36 % Favored : 91.37 % Rotamer: Outliers : 4.70 % Allowed : 27.25 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.16), residues: 2597 helix: 1.29 (0.18), residues: 883 sheet: 0.49 (0.20), residues: 668 loop : -3.27 (0.15), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 243 TYR 0.034 0.002 TYR E 58 PHE 0.020 0.002 PHE A 484 TRP 0.031 0.002 TRP A 119 HIS 0.010 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00381 (21456) covalent geometry : angle 0.79666 (29068) hydrogen bonds : bond 0.04315 ( 972) hydrogen bonds : angle 5.26308 ( 2847) link_BETA1-4 : bond 0.00404 ( 6) link_BETA1-4 : angle 2.56587 ( 18) link_NAG-ASN : bond 0.00669 ( 3) link_NAG-ASN : angle 3.30848 ( 9) *********************** 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 427 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 320 time to evaluate : 0.893 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 375 ILE cc_start: 0.5926 (mt) cc_final: 0.5328 (mt) REVERT: A 442 LEU cc_start: 0.0492 (OUTLIER) cc_final: -0.0653 (mt) REVERT: B 32 GLN cc_start: 0.7456 (tp40) cc_final: 0.7223 (tt0) REVERT: C 70 LYS cc_start: 0.8154 (tptm) cc_final: 0.7677 (tppt) REVERT: C 74 LEU cc_start: 0.8391 (mt) cc_final: 0.7945 (tt) REVERT: C 210 MET cc_start: 0.2491 (mmm) cc_final: 0.2180 (mmm) REVERT: C 226 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6491 (tm-30) REVERT: D 49 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (p0) REVERT: E 70 MET cc_start: 0.1195 (mmm) cc_final: 0.0896 (mmm) REVERT: F 78 PHE cc_start: 0.3046 (m-80) cc_final: 0.2776 (m-10) REVERT: F 90 ILE cc_start: 0.6956 (mt) cc_final: 0.6728 (mp) REVERT: G 117 LYS cc_start: 0.6493 (tptt) cc_final: 0.5981 (tptt) REVERT: G 124 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.5898 (t0) REVERT: G 162 MET cc_start: 0.6810 (ptp) cc_final: 0.5771 (ttp) REVERT: H 151 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.6630 (t-100) REVERT: J 74 LEU cc_start: -0.0377 (OUTLIER) cc_final: -0.1005 (tp) REVERT: K 154 GLN cc_start: 0.8672 (tt0) cc_final: 0.8437 (tm-30) REVERT: K 189 GLU cc_start: 0.7890 (mp0) cc_final: 0.7451 (mp0) REVERT: K 251 LEU cc_start: 0.2290 (OUTLIER) cc_final: 0.2066 (tp) outliers start: 107 outliers final: 35 residues processed: 403 average time/residue: 0.1649 time to fit residues: 101.2363 Evaluate side-chains 300 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 97 VAL 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 649 VAL Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 111 ASP 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 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 174 LEU Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 208 HIS 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 21 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 9 optimal weight: 0.0270 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 521 ASN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 786 HIS ** A 829 GLN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS C 230 HIS ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN 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 = 0.4120 r_free = 0.4120 target = 0.099507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.082283 restraints weight = 83850.518| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 5.06 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3911 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21465 Z= 0.169 Angle : 0.777 13.734 29095 Z= 0.371 Chirality : 0.046 0.489 3279 Planarity : 0.005 0.064 3679 Dihedral : 5.164 56.662 3028 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.16 % Favored : 91.57 % Rotamer: Outliers : 4.44 % Allowed : 28.00 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2597 helix: 1.37 (0.18), residues: 880 sheet: 0.54 (0.20), residues: 676 loop : -3.26 (0.15), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 102 TYR 0.030 0.002 TYR A 817 PHE 0.025 0.002 PHE E 67 TRP 0.019 0.002 TRP F 74 HIS 0.012 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00367 (21456) covalent geometry : angle 0.76637 (29068) hydrogen bonds : bond 0.03851 ( 972) hydrogen bonds : angle 4.99972 ( 2847) link_BETA1-4 : bond 0.00899 ( 6) link_BETA1-4 : angle 2.90512 ( 18) link_NAG-ASN : bond 0.02051 ( 3) link_NAG-ASN : angle 6.08555 ( 9) *********************** 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 395 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 294 time to evaluate : 0.775 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: A 96 ASP cc_start: 0.7348 (m-30) cc_final: 0.6744 (t70) REVERT: A 177 MET cc_start: 0.6891 (mtp) cc_final: 0.6419 (mtt) REVERT: A 294 HIS cc_start: 0.6232 (t-170) cc_final: 0.5317 (t-90) REVERT: A 442 LEU cc_start: 0.0561 (OUTLIER) cc_final: 0.0328 (mp) REVERT: A 470 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8406 (mt-10) REVERT: A 689 ASP cc_start: 0.4044 (t0) cc_final: 0.3434 (t0) REVERT: A 690 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3406 (mt) REVERT: A 847 MET cc_start: 0.0789 (OUTLIER) cc_final: -0.0127 (ptt) REVERT: B 32 GLN cc_start: 0.7342 (tp40) cc_final: 0.7099 (tt0) REVERT: C 70 LYS cc_start: 0.8146 (tptm) cc_final: 0.7573 (tppt) REVERT: C 81 ASN cc_start: 0.5895 (m-40) cc_final: 0.5515 (t0) REVERT: C 147 ARG cc_start: 0.1521 (mtt180) cc_final: -0.1001 (mtp85) REVERT: C 151 MET cc_start: 0.3984 (mmt) cc_final: 0.3237 (tpp) REVERT: C 210 MET cc_start: 0.2932 (mmm) cc_final: 0.2560 (mmm) REVERT: C 226 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6356 (tm-30) REVERT: E 70 MET cc_start: 0.2053 (mmm) cc_final: 0.1429 (mmm) REVERT: F 90 ILE cc_start: 0.6970 (mt) cc_final: 0.6744 (mp) REVERT: G 117 LYS cc_start: 0.6659 (tptt) cc_final: 0.6251 (tptt) REVERT: G 124 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.6508 (t0) REVERT: G 162 MET cc_start: 0.6995 (ptp) cc_final: 0.5845 (ttp) REVERT: H 94 GLN cc_start: 0.5376 (OUTLIER) cc_final: 0.4688 (tm-30) REVERT: H 132 PHE cc_start: 0.4440 (t80) cc_final: 0.4171 (t80) REVERT: H 166 GLU cc_start: 0.8472 (mp0) cc_final: 0.8080 (mp0) REVERT: J 74 LEU cc_start: 0.0403 (OUTLIER) cc_final: 0.0013 (tp) REVERT: K 9 ASP cc_start: 0.8243 (t70) cc_final: 0.7755 (p0) REVERT: K 166 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7666 (tp-100) REVERT: K 251 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1942 (tp) outliers start: 101 outliers final: 47 residues processed: 371 average time/residue: 0.1437 time to fit residues: 82.4758 Evaluate side-chains 302 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 248 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 216 SER 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 545 LEU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 165 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 82 MET 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 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 80 THR Chi-restraints excluded: chain G residue 89 ILE 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 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 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 97 ARG 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 167 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 245 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 207 optimal weight: 0.0470 chunk 190 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 238 HIS B 253 ASN C 39 GLN C 231 GLN D 51 GLN G 163 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.098935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082007 restraints weight = 86431.370| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 5.13 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4255 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21465 Z= 0.172 Angle : 0.791 13.021 29095 Z= 0.377 Chirality : 0.044 0.188 3279 Planarity : 0.005 0.060 3679 Dihedral : 5.166 63.565 3028 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.59 % Favored : 91.14 % Rotamer: Outliers : 5.19 % Allowed : 27.08 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2597 helix: 1.16 (0.17), residues: 889 sheet: 0.49 (0.20), residues: 679 loop : -3.24 (0.15), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 527 TYR 0.020 0.002 TYR H 87 PHE 0.037 0.002 PHE A 324 TRP 0.018 0.002 TRP A 119 HIS 0.009 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00385 (21456) covalent geometry : angle 0.78605 (29068) hydrogen bonds : bond 0.03531 ( 972) hydrogen bonds : angle 4.87329 ( 2847) link_BETA1-4 : bond 0.00220 ( 6) link_BETA1-4 : angle 2.15193 ( 18) link_NAG-ASN : bond 0.02020 ( 3) link_NAG-ASN : angle 4.00895 ( 9) *********************** 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 423 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 305 time to evaluate : 0.678 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 96 ASP cc_start: 0.7708 (m-30) cc_final: 0.6909 (t70) REVERT: A 117 LEU cc_start: 0.6055 (tp) cc_final: 0.5653 (tp) REVERT: A 148 LYS cc_start: 0.8000 (tppt) cc_final: 0.7749 (mmmt) REVERT: A 174 HIS cc_start: 0.7587 (t70) cc_final: 0.6960 (t70) REVERT: A 442 LEU cc_start: 0.1386 (OUTLIER) cc_final: 0.1089 (mp) REVERT: A 689 ASP cc_start: 0.4407 (t0) cc_final: 0.4083 (t0) REVERT: A 798 THR cc_start: 0.5162 (OUTLIER) cc_final: 0.4915 (p) REVERT: A 889 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 919 MET cc_start: 0.6008 (mmt) cc_final: 0.5709 (mmt) REVERT: C 70 LYS cc_start: 0.8166 (tptm) cc_final: 0.7598 (tppt) REVERT: C 81 ASN cc_start: 0.5947 (m-40) cc_final: 0.5684 (t0) REVERT: C 110 MET cc_start: 0.0051 (ptp) cc_final: -0.0314 (ptp) REVERT: C 130 MET cc_start: 0.6034 (tmm) cc_final: 0.5791 (tmm) REVERT: C 135 PHE cc_start: 0.4249 (OUTLIER) cc_final: 0.2501 (t80) REVERT: C 147 ARG cc_start: 0.1829 (mtt180) cc_final: -0.0754 (mtp85) REVERT: C 182 ILE cc_start: 0.3959 (mm) cc_final: 0.3633 (mm) REVERT: C 203 MET cc_start: 0.0856 (mmt) cc_final: -0.0293 (mmt) REVERT: C 226 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6757 (tm-30) REVERT: D 49 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8405 (p0) REVERT: D 154 MET cc_start: 0.5233 (tpt) cc_final: 0.4694 (tpp) REVERT: E 70 MET cc_start: 0.2104 (mmm) cc_final: 0.1387 (mmm) REVERT: F 90 ILE cc_start: 0.7206 (mt) cc_final: 0.6992 (mp) REVERT: G 45 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7631 (t80) REVERT: G 118 MET cc_start: -0.1251 (pmm) cc_final: -0.1730 (pmm) REVERT: G 162 MET cc_start: 0.7098 (ptp) cc_final: 0.6404 (ttm) REVERT: H 14 MET cc_start: 0.4236 (tmm) cc_final: 0.3919 (tmm) REVERT: H 94 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6441 (tm-30) REVERT: H 132 PHE cc_start: 0.4688 (t80) cc_final: 0.4420 (t80) REVERT: H 163 ASP cc_start: 0.6660 (p0) cc_final: 0.6292 (p0) REVERT: H 166 GLU cc_start: 0.8399 (mp0) cc_final: 0.7885 (mp0) REVERT: J 74 LEU cc_start: 0.0780 (OUTLIER) cc_final: 0.0189 (tp) REVERT: K 9 ASP cc_start: 0.8196 (t70) cc_final: 0.7740 (p0) REVERT: K 166 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7952 (tp-100) REVERT: K 189 GLU cc_start: 0.7885 (mp0) cc_final: 0.7661 (mm-30) REVERT: K 251 LEU cc_start: 0.2391 (OUTLIER) cc_final: 0.2019 (tp) outliers start: 118 outliers final: 60 residues processed: 390 average time/residue: 0.1445 time to fit residues: 88.4012 Evaluate side-chains 335 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL 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 150 THR Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 LEU 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 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU 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 165 TRP Chi-restraints excluded: chain C residue 176 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 60 ILE 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 95 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 126 ILE 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 182 THR Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 97 ARG 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 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 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 33 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 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 832 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 167 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN K 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.098238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.081552 restraints weight = 87196.269| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 5.59 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4472 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21465 Z= 0.153 Angle : 0.774 11.419 29095 Z= 0.371 Chirality : 0.044 0.237 3279 Planarity : 0.005 0.061 3679 Dihedral : 4.758 59.918 3028 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.28 % Favored : 91.41 % Rotamer: Outliers : 4.75 % Allowed : 28.09 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2597 helix: 1.17 (0.17), residues: 891 sheet: 0.55 (0.20), residues: 671 loop : -3.12 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 95 TYR 0.031 0.002 TYR B 147 PHE 0.053 0.002 PHE E 67 TRP 0.035 0.002 TRP C 15 HIS 0.019 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00344 (21456) covalent geometry : angle 0.76983 (29068) hydrogen bonds : bond 0.03458 ( 972) hydrogen bonds : angle 4.81365 ( 2847) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.79570 ( 18) link_NAG-ASN : bond 0.00386 ( 3) link_NAG-ASN : angle 3.96142 ( 9) *********************** 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 407 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 299 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: A 174 HIS cc_start: 0.7777 (t70) cc_final: 0.7219 (t70) REVERT: A 177 MET cc_start: 0.6783 (mtt) cc_final: 0.6508 (mtt) REVERT: A 442 LEU cc_start: 0.1853 (OUTLIER) cc_final: 0.1595 (mp) REVERT: A 611 TRP cc_start: 0.3846 (m-90) cc_final: 0.3231 (m-90) REVERT: A 848 GLU cc_start: 0.6095 (pm20) cc_final: 0.5577 (pm20) REVERT: A 889 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 33 ILE cc_start: 0.5493 (mt) cc_final: 0.5293 (mt) REVERT: C 39 GLN cc_start: 0.6730 (pp30) cc_final: 0.6523 (mm-40) REVERT: C 70 LYS cc_start: 0.8185 (tptm) cc_final: 0.7631 (tppt) REVERT: C 81 ASN cc_start: 0.6026 (m-40) cc_final: 0.5760 (t0) REVERT: C 135 PHE cc_start: 0.4345 (OUTLIER) cc_final: 0.2749 (t80) REVERT: C 147 ARG cc_start: 0.2157 (mtt180) cc_final: -0.0248 (mtp85) REVERT: C 182 ILE cc_start: 0.3840 (mm) cc_final: 0.3557 (mm) REVERT: C 226 GLU cc_start: 0.7909 (mt-10) cc_final: 0.6527 (tp30) REVERT: D 154 MET cc_start: 0.4648 (tpt) cc_final: 0.4230 (tpp) REVERT: E 70 MET cc_start: 0.1984 (mmm) cc_final: 0.1496 (mmm) REVERT: G 45 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7814 (t80) REVERT: G 106 ASP cc_start: 0.5871 (p0) cc_final: 0.5653 (p0) REVERT: G 118 MET cc_start: -0.1023 (pmm) cc_final: -0.1524 (pmm) REVERT: G 162 MET cc_start: 0.7379 (ptp) cc_final: 0.5924 (ttp) REVERT: H 132 PHE cc_start: 0.5136 (t80) cc_final: 0.4766 (t80) REVERT: H 163 ASP cc_start: 0.6872 (p0) cc_final: 0.6521 (p0) REVERT: H 166 GLU cc_start: 0.8432 (mp0) cc_final: 0.7850 (mp0) REVERT: J 74 LEU cc_start: 0.2034 (OUTLIER) cc_final: 0.1823 (tp) REVERT: J 178 LEU cc_start: 0.4557 (OUTLIER) cc_final: 0.4244 (pp) REVERT: K 9 ASP cc_start: 0.8201 (t70) cc_final: 0.7694 (p0) REVERT: K 154 GLN cc_start: 0.8813 (pt0) cc_final: 0.8052 (mm-40) REVERT: K 166 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7879 (tp-100) REVERT: K 251 LEU cc_start: 0.1748 (OUTLIER) cc_final: 0.1485 (tp) outliers start: 108 outliers final: 63 residues processed: 384 average time/residue: 0.1382 time to fit residues: 83.5276 Evaluate side-chains 330 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 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 332 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 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 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 246 SER Chi-restraints excluded: chain C residue 27 VAL 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 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 237 VAL 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 60 ILE Chi-restraints excluded: chain F residue 85 PHE 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 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 97 ARG 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 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 178 LEU 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 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 99 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS ** A 318 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 242 ASN C 231 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.098393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082049 restraints weight = 87837.454| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 5.14 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4798 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21465 Z= 0.171 Angle : 0.796 16.539 29095 Z= 0.379 Chirality : 0.045 0.193 3279 Planarity : 0.005 0.118 3679 Dihedral : 4.720 58.410 3028 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.66 % Favored : 91.03 % Rotamer: Outliers : 4.84 % Allowed : 28.66 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2597 helix: 1.10 (0.17), residues: 895 sheet: 0.61 (0.20), residues: 660 loop : -3.03 (0.16), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 80 TYR 0.026 0.002 TYR B 147 PHE 0.048 0.002 PHE B 230 TRP 0.050 0.002 TRP A 163 HIS 0.014 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00374 (21456) covalent geometry : angle 0.79233 (29068) hydrogen bonds : bond 0.03526 ( 972) hydrogen bonds : angle 4.81540 ( 2847) link_BETA1-4 : bond 0.00389 ( 6) link_BETA1-4 : angle 1.59054 ( 18) link_NAG-ASN : bond 0.00791 ( 3) link_NAG-ASN : angle 3.66764 ( 9) *********************** 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 436 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 326 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5977 (m-10) REVERT: A 174 HIS cc_start: 0.7780 (t70) cc_final: 0.7214 (t70) REVERT: A 177 MET cc_start: 0.6758 (mtt) cc_final: 0.6296 (mtt) REVERT: A 310 LEU cc_start: 0.6720 (mm) cc_final: 0.6167 (pp) REVERT: A 415 ASP cc_start: 0.8345 (m-30) cc_final: 0.8123 (p0) REVERT: A 442 LEU cc_start: 0.2542 (OUTLIER) cc_final: 0.2192 (mp) REVERT: A 556 LEU cc_start: 0.6909 (mt) cc_final: 0.6684 (mp) REVERT: A 632 MET cc_start: 0.3576 (mmt) cc_final: 0.3108 (tpp) REVERT: A 871 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4346 (pp) REVERT: A 889 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 33 ILE cc_start: 0.5643 (mt) cc_final: 0.5411 (mt) REVERT: B 226 MET cc_start: 0.3505 (OUTLIER) cc_final: 0.3221 (ttm) REVERT: C 14 LEU cc_start: 0.5571 (tt) cc_final: 0.5338 (mt) REVERT: C 70 LYS cc_start: 0.8104 (tptm) cc_final: 0.7537 (tppt) REVERT: C 110 MET cc_start: 0.0339 (OUTLIER) cc_final: 0.0094 (ttp) REVERT: C 135 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.3263 (t80) REVERT: C 147 ARG cc_start: 0.2273 (mtt180) cc_final: -0.0165 (mtp-110) REVERT: C 151 MET cc_start: 0.4477 (mmt) cc_final: 0.3727 (tpp) REVERT: C 203 MET cc_start: -0.0445 (mmt) cc_final: -0.0689 (mmp) REVERT: C 210 MET cc_start: 0.3325 (mmm) cc_final: 0.2858 (mmm) REVERT: D 101 MET cc_start: 0.6869 (mmt) cc_final: 0.6610 (mmm) REVERT: D 137 LEU cc_start: 0.8275 (tp) cc_final: 0.8024 (mt) REVERT: D 154 MET cc_start: 0.4666 (tpt) cc_final: 0.3808 (mtm) REVERT: E 58 TYR cc_start: 0.3672 (t80) cc_final: 0.3121 (m-80) REVERT: E 70 MET cc_start: 0.2347 (mmm) cc_final: 0.1776 (mmm) REVERT: F 89 LEU cc_start: 0.7340 (mt) cc_final: 0.6931 (pp) REVERT: G 45 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8039 (t80) REVERT: G 117 LYS cc_start: 0.7046 (tptt) cc_final: 0.6730 (tptt) REVERT: G 118 MET cc_start: -0.0612 (pmm) cc_final: -0.0991 (pmm) REVERT: G 162 MET cc_start: 0.7367 (ptp) cc_final: 0.5938 (ttp) REVERT: H 132 PHE cc_start: 0.5649 (t80) cc_final: 0.5415 (t80) REVERT: H 163 ASP cc_start: 0.6809 (p0) cc_final: 0.6539 (p0) REVERT: H 166 GLU cc_start: 0.8489 (mp0) cc_final: 0.7885 (mp0) REVERT: J 63 ASP cc_start: 0.7651 (t0) cc_final: 0.6187 (t0) REVERT: J 74 LEU cc_start: 0.2520 (OUTLIER) cc_final: 0.2280 (tp) REVERT: J 151 ASP cc_start: 0.4806 (m-30) cc_final: 0.3843 (t0) REVERT: J 178 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4157 (pp) REVERT: K 9 ASP cc_start: 0.8336 (t70) cc_final: 0.7770 (p0) REVERT: K 154 GLN cc_start: 0.8912 (pt0) cc_final: 0.8105 (mm-40) REVERT: K 166 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7862 (tp-100) REVERT: K 181 HIS cc_start: 0.4948 (t70) cc_final: 0.4658 (t-170) REVERT: K 251 LEU cc_start: 0.1799 (OUTLIER) cc_final: 0.1471 (tp) outliers start: 110 outliers final: 66 residues processed: 410 average time/residue: 0.1266 time to fit residues: 82.7877 Evaluate side-chains 355 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL 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 134 VAL Chi-restraints excluded: chain A residue 173 ILE 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 312 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 700 ILE 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 A residue 910 ILE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU 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 63 GLU Chi-restraints excluded: chain C residue 110 MET 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 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 55 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 85 PHE 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 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 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 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 178 LEU 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 6 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 208 optimal weight: 0.0030 chunk 164 optimal weight: 8.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 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 = 0.4105 r_free = 0.4105 target = 0.098186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082061 restraints weight = 89251.504| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 5.20 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.9569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21465 Z= 0.171 Angle : 0.833 14.540 29095 Z= 0.396 Chirality : 0.046 0.219 3279 Planarity : 0.005 0.063 3679 Dihedral : 4.845 58.586 3028 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.86 % Favored : 91.80 % Rotamer: Outliers : 4.92 % Allowed : 29.85 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2597 helix: 0.94 (0.17), residues: 894 sheet: 0.56 (0.20), residues: 663 loop : -3.02 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 97 TYR 0.019 0.002 TYR A 419 PHE 0.046 0.002 PHE B 230 TRP 0.045 0.002 TRP A 992 HIS 0.013 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00381 (21456) covalent geometry : angle 0.83008 (29068) hydrogen bonds : bond 0.03632 ( 972) hydrogen bonds : angle 4.96878 ( 2847) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.67307 ( 18) link_NAG-ASN : bond 0.00876 ( 3) link_NAG-ASN : angle 3.58509 ( 9) *********************** 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 432 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 320 time to evaluate : 0.924 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 47 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: A 58 THR cc_start: 0.6846 (p) cc_final: 0.6405 (p) REVERT: A 174 HIS cc_start: 0.7699 (t70) cc_final: 0.7131 (t70) REVERT: A 177 MET cc_start: 0.6746 (mtt) cc_final: 0.6269 (mtt) REVERT: A 221 GLN cc_start: 0.6726 (pm20) cc_final: 0.6505 (pp30) REVERT: A 310 LEU cc_start: 0.6803 (mm) cc_final: 0.6197 (pp) REVERT: A 318 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: A 442 LEU cc_start: 0.3450 (OUTLIER) cc_final: 0.3056 (mp) REVERT: A 889 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 923 TYR cc_start: 0.7555 (t80) cc_final: 0.7245 (t80) REVERT: A 957 LYS cc_start: 0.5396 (mtmt) cc_final: 0.4583 (ptpt) REVERT: C 14 LEU cc_start: 0.6051 (tt) cc_final: 0.5681 (mt) REVERT: C 39 GLN cc_start: 0.7064 (pp30) cc_final: 0.6858 (mm-40) REVERT: C 70 LYS cc_start: 0.8151 (tptm) cc_final: 0.7583 (tppt) REVERT: C 147 ARG cc_start: 0.1623 (mtt180) cc_final: 0.0427 (tmm-80) REVERT: C 151 MET cc_start: 0.4963 (mmt) cc_final: 0.4369 (tpp) REVERT: C 210 MET cc_start: 0.3512 (mmm) cc_final: 0.3043 (mmm) REVERT: C 226 GLU cc_start: 0.8295 (mt-10) cc_final: 0.6632 (tp30) REVERT: D 49 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8583 (p0) REVERT: D 137 LEU cc_start: 0.8026 (tp) cc_final: 0.7765 (mt) REVERT: E 58 TYR cc_start: 0.4184 (OUTLIER) cc_final: 0.3625 (m-80) REVERT: F 89 LEU cc_start: 0.7441 (mt) cc_final: 0.7032 (pp) REVERT: G 45 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8322 (t80) REVERT: G 117 LYS cc_start: 0.7231 (tptt) cc_final: 0.6859 (tptt) REVERT: G 118 MET cc_start: 0.0443 (pmm) cc_final: -0.0211 (pmm) REVERT: G 162 MET cc_start: 0.7524 (ptp) cc_final: 0.6018 (ttp) REVERT: H 132 PHE cc_start: 0.5702 (t80) cc_final: 0.5447 (t80) REVERT: H 163 ASP cc_start: 0.6792 (p0) cc_final: 0.6505 (p0) REVERT: H 166 GLU cc_start: 0.8563 (mp0) cc_final: 0.7906 (mp0) REVERT: J 74 LEU cc_start: 0.2808 (OUTLIER) cc_final: 0.2519 (tp) REVERT: J 151 ASP cc_start: 0.5376 (m-30) cc_final: 0.4461 (t0) REVERT: J 178 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.3999 (pp) REVERT: K 9 ASP cc_start: 0.8378 (t70) cc_final: 0.7795 (p0) REVERT: K 154 GLN cc_start: 0.8973 (pt0) cc_final: 0.8124 (mm-40) REVERT: K 166 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7879 (tp-100) REVERT: K 251 LEU cc_start: 0.2243 (OUTLIER) cc_final: 0.1975 (tp) outliers start: 112 outliers final: 73 residues processed: 403 average time/residue: 0.1410 time to fit residues: 89.6844 Evaluate side-chains 379 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 297 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 145 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 312 LEU Chi-restraints excluded: chain A residue 318 GLN 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 525 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 873 LEU 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 B residue 111 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 116 THR 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 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 55 VAL Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 96 TYR 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 174 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 208 HIS 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 J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 66 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 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.0060 chunk 53 optimal weight: 0.0060 chunk 81 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 253 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4812 ------------------------------------------------------------------------------- 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 A 222 HIS ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** 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 = 0.4113 r_free = 0.4113 target = 0.098576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.082503 restraints weight = 89485.917| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 5.21 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5154 moved from start: 0.9927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21465 Z= 0.136 Angle : 0.794 12.627 29095 Z= 0.373 Chirality : 0.044 0.281 3279 Planarity : 0.005 0.062 3679 Dihedral : 4.691 58.548 3028 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.78 % Favored : 91.88 % Rotamer: Outliers : 3.78 % Allowed : 30.73 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2597 helix: 1.11 (0.17), residues: 894 sheet: 0.61 (0.20), residues: 650 loop : -2.91 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.021 0.001 TYR B 8 PHE 0.057 0.002 PHE B 230 TRP 0.035 0.002 TRP H 197 HIS 0.013 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00296 (21456) covalent geometry : angle 0.79085 (29068) hydrogen bonds : bond 0.03254 ( 972) hydrogen bonds : angle 4.69867 ( 2847) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 1.52718 ( 18) link_NAG-ASN : bond 0.00728 ( 3) link_NAG-ASN : angle 3.33147 ( 9) *********************** 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 414 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 328 time to evaluate : 0.581 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 47 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.5993 (m-80) REVERT: A 92 LEU cc_start: 0.7551 (tt) cc_final: 0.7259 (tp) REVERT: A 174 HIS cc_start: 0.7692 (t70) cc_final: 0.7142 (t70) REVERT: A 177 MET cc_start: 0.6699 (mtt) cc_final: 0.6258 (mtt) REVERT: A 221 GLN cc_start: 0.6740 (pm20) cc_final: 0.6496 (pp30) REVERT: A 310 LEU cc_start: 0.6752 (mm) cc_final: 0.6127 (pp) REVERT: A 442 LEU cc_start: 0.3507 (OUTLIER) cc_final: 0.3190 (mp) REVERT: A 632 MET cc_start: 0.3315 (mmt) cc_final: 0.3025 (tpp) REVERT: A 863 ILE cc_start: 0.7863 (tp) cc_final: 0.7563 (tp) REVERT: A 889 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 923 TYR cc_start: 0.7675 (t80) cc_final: 0.7407 (t80) REVERT: A 957 LYS cc_start: 0.5492 (mtmt) cc_final: 0.5232 (ptpt) REVERT: B 33 ILE cc_start: 0.6267 (mt) cc_final: 0.5837 (tp) REVERT: B 234 MET cc_start: 0.6510 (ptt) cc_final: 0.6278 (ptt) REVERT: C 14 LEU cc_start: 0.5967 (tt) cc_final: 0.5764 (mt) REVERT: C 70 LYS cc_start: 0.8106 (tptm) cc_final: 0.7541 (tppt) REVERT: C 81 ASN cc_start: 0.6064 (m-40) cc_final: 0.5848 (t0) REVERT: C 147 ARG cc_start: 0.1469 (mtt180) cc_final: 0.0299 (ttp-170) REVERT: C 151 MET cc_start: 0.4959 (mmt) cc_final: 0.4329 (tpp) REVERT: C 210 MET cc_start: 0.3532 (mmm) cc_final: 0.3079 (mmm) REVERT: D 49 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8515 (p0) REVERT: E 58 TYR cc_start: 0.4273 (OUTLIER) cc_final: 0.3635 (m-80) REVERT: E 70 MET cc_start: 0.2671 (mmm) cc_final: 0.2377 (mmt) REVERT: F 89 LEU cc_start: 0.7594 (mt) cc_final: 0.7152 (pp) REVERT: G 45 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8307 (t80) REVERT: G 117 LYS cc_start: 0.7207 (tptt) cc_final: 0.6862 (tptt) REVERT: G 118 MET cc_start: 0.0658 (pmm) cc_final: -0.0004 (pmm) REVERT: G 130 GLU cc_start: 0.8487 (mp0) cc_final: 0.8257 (mp0) REVERT: G 140 MET cc_start: 0.5584 (tpt) cc_final: 0.5220 (tpt) REVERT: G 162 MET cc_start: 0.7477 (ptp) cc_final: 0.5816 (ttp) REVERT: G 165 MET cc_start: -0.1617 (mmt) cc_final: -0.1877 (mmt) REVERT: H 70 MET cc_start: 0.3655 (ppp) cc_final: 0.3410 (ppp) REVERT: H 94 GLN cc_start: 0.6527 (tm-30) cc_final: 0.6027 (tm-30) REVERT: H 132 PHE cc_start: 0.5726 (t80) cc_final: 0.5439 (t80) REVERT: H 163 ASP cc_start: 0.6766 (p0) cc_final: 0.6465 (p0) REVERT: H 166 GLU cc_start: 0.8577 (mp0) cc_final: 0.7928 (mp0) REVERT: J 74 LEU cc_start: 0.2774 (OUTLIER) cc_final: 0.2561 (tp) REVERT: J 151 ASP cc_start: 0.5257 (m-30) cc_final: 0.4397 (t0) REVERT: J 178 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.4222 (pp) REVERT: K 154 GLN cc_start: 0.8987 (pt0) cc_final: 0.8151 (mm-40) REVERT: K 166 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7740 (tp-100) REVERT: K 189 GLU cc_start: 0.8863 (mp0) cc_final: 0.8503 (tp30) REVERT: K 251 LEU cc_start: 0.2171 (OUTLIER) cc_final: 0.1751 (tp) outliers start: 86 outliers final: 65 residues processed: 394 average time/residue: 0.1342 time to fit residues: 83.6871 Evaluate side-chains 377 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ILE 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 312 LEU 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 442 LEU Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 27 VAL 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 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 E residue 55 VAL Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE 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 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 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 J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 71 PHE 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 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 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 127 optimal weight: 0.6980 chunk 221 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 428 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 GLN A 984 GLN ** B 32 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** E 94 ASN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.099742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083029 restraints weight = 92683.378| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.55 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 1.0431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21465 Z= 0.143 Angle : 0.817 14.844 29095 Z= 0.387 Chirality : 0.045 0.297 3279 Planarity : 0.005 0.071 3679 Dihedral : 4.742 58.929 3028 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.61 % Rotamer: Outliers : 3.82 % Allowed : 31.16 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2597 helix: 1.06 (0.17), residues: 901 sheet: 0.58 (0.20), residues: 656 loop : -2.98 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 946 TYR 0.017 0.001 TYR A 793 PHE 0.053 0.002 PHE B 230 TRP 0.035 0.002 TRP H 197 HIS 0.025 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00318 (21456) covalent geometry : angle 0.81442 (29068) hydrogen bonds : bond 0.03337 ( 972) hydrogen bonds : angle 4.71540 ( 2847) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 1.54067 ( 18) link_NAG-ASN : bond 0.00749 ( 3) link_NAG-ASN : angle 3.35494 ( 9) *********************** 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 409 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 322 time to evaluate : 0.780 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: A 47 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: A 174 HIS cc_start: 0.7768 (t70) cc_final: 0.7244 (t70) REVERT: A 177 MET cc_start: 0.6728 (mtt) cc_final: 0.6156 (mtt) REVERT: A 310 LEU cc_start: 0.6767 (mm) cc_final: 0.6115 (pp) REVERT: B 234 MET cc_start: 0.6657 (ptt) cc_final: 0.6434 (ptt) REVERT: C 70 LYS cc_start: 0.8207 (tptm) cc_final: 0.7604 (tppt) REVERT: C 147 ARG cc_start: 0.1728 (mtt180) cc_final: 0.0889 (ttp-170) REVERT: C 151 MET cc_start: 0.5101 (mmt) cc_final: 0.4479 (tpp) REVERT: C 210 MET cc_start: 0.3517 (mmm) cc_final: 0.2756 (mmm) REVERT: E 58 TYR cc_start: 0.4297 (OUTLIER) cc_final: 0.3669 (m-80) REVERT: E 70 MET cc_start: 0.3193 (mmm) cc_final: 0.2560 (mmt) REVERT: F 89 LEU cc_start: 0.7669 (mt) cc_final: 0.7234 (pp) REVERT: G 45 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8464 (t80) REVERT: G 117 LYS cc_start: 0.7307 (tptt) cc_final: 0.6954 (tptt) REVERT: G 118 MET cc_start: 0.0424 (pmm) cc_final: -0.0295 (pmm) REVERT: G 130 GLU cc_start: 0.8509 (mp0) cc_final: 0.8292 (mp0) REVERT: G 140 MET cc_start: 0.5887 (tpt) cc_final: 0.5439 (tpt) REVERT: G 162 MET cc_start: 0.7493 (ptp) cc_final: 0.5971 (ttp) REVERT: H 94 GLN cc_start: 0.6548 (tm-30) cc_final: 0.6155 (tm-30) REVERT: H 163 ASP cc_start: 0.6954 (p0) cc_final: 0.6646 (p0) REVERT: H 166 GLU cc_start: 0.8638 (mp0) cc_final: 0.7990 (mp0) REVERT: H 174 LEU cc_start: 0.8038 (mt) cc_final: 0.7735 (mt) REVERT: J 74 LEU cc_start: 0.2788 (OUTLIER) cc_final: 0.2536 (tp) REVERT: J 151 ASP cc_start: 0.5230 (m-30) cc_final: 0.4527 (t0) REVERT: J 178 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.4272 (pp) REVERT: J 197 GLU cc_start: 0.6168 (pp20) cc_final: 0.5903 (pp20) REVERT: K 9 ASP cc_start: 0.8679 (t0) cc_final: 0.7972 (p0) REVERT: K 154 GLN cc_start: 0.9034 (pt0) cc_final: 0.8252 (mm-40) REVERT: K 166 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7781 (tp-100) REVERT: K 189 GLU cc_start: 0.8865 (mp0) cc_final: 0.8515 (tp30) REVERT: K 251 LEU cc_start: 0.1926 (OUTLIER) cc_final: 0.1685 (tp) outliers start: 87 outliers final: 64 residues processed: 386 average time/residue: 0.1306 time to fit residues: 80.7493 Evaluate side-chains 372 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 302 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 312 LEU 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 458 VAL Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 784 ILE 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 935 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 237 VAL 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 55 VAL Chi-restraints excluded: chain E residue 58 TYR 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 85 PHE 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 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 208 HIS 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 J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR 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 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 559 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.098369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.082118 restraints weight = 93932.046| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 5.35 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 1.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21465 Z= 0.164 Angle : 0.855 22.551 29095 Z= 0.408 Chirality : 0.046 0.233 3279 Planarity : 0.005 0.069 3679 Dihedral : 4.887 59.008 3028 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.61 % Rotamer: Outliers : 3.78 % Allowed : 31.65 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2597 helix: 1.10 (0.18), residues: 887 sheet: 0.55 (0.20), residues: 667 loop : -2.96 (0.16), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 946 TYR 0.038 0.002 TYR B 214 PHE 0.052 0.002 PHE B 230 TRP 0.035 0.002 TRP H 197 HIS 0.014 0.002 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00367 (21456) covalent geometry : angle 0.85250 (29068) hydrogen bonds : bond 0.03542 ( 972) hydrogen bonds : angle 4.79724 ( 2847) link_BETA1-4 : bond 0.00397 ( 6) link_BETA1-4 : angle 1.55801 ( 18) link_NAG-ASN : bond 0.01039 ( 3) link_NAG-ASN : angle 3.59119 ( 9) ********************** 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 429 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 0.737 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: A 47 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: A 90 MET cc_start: 0.8131 (tmm) cc_final: 0.7801 (tmm) REVERT: A 92 LEU cc_start: 0.8367 (tp) cc_final: 0.7816 (tp) REVERT: A 174 HIS cc_start: 0.7733 (t70) cc_final: 0.7174 (t70) REVERT: A 177 MET cc_start: 0.6770 (mtt) cc_final: 0.6188 (mtt) REVERT: A 310 LEU cc_start: 0.6979 (mm) cc_final: 0.6316 (pp) REVERT: A 457 MET cc_start: 0.6755 (mmm) cc_final: 0.6322 (mmt) REVERT: A 870 ILE cc_start: 0.8051 (mt) cc_final: 0.7738 (pt) REVERT: A 889 GLN cc_start: 0.6967 (tm-30) cc_final: 0.6731 (tm-30) REVERT: A 930 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.4781 (tp30) REVERT: B 32 GLN cc_start: 0.6517 (pp30) cc_final: 0.6244 (pp30) REVERT: C 70 LYS cc_start: 0.8289 (tptm) cc_final: 0.7679 (tppt) REVERT: C 147 ARG cc_start: 0.2290 (mtt180) cc_final: 0.1400 (ttp-170) REVERT: C 151 MET cc_start: 0.5115 (mmt) cc_final: 0.4615 (tpp) REVERT: C 210 MET cc_start: 0.3533 (mmm) cc_final: 0.3112 (mmm) REVERT: D 49 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8585 (p0) REVERT: E 58 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4401 (m-80) REVERT: F 89 LEU cc_start: 0.7775 (mt) cc_final: 0.7395 (pp) REVERT: G 117 LYS cc_start: 0.7403 (tptt) cc_final: 0.7185 (tptt) REVERT: G 118 MET cc_start: 0.0770 (pmm) cc_final: -0.0057 (pmm) REVERT: G 140 MET cc_start: 0.6618 (tpt) cc_final: 0.6168 (tpt) REVERT: G 162 MET cc_start: 0.7547 (ptp) cc_final: 0.5607 (ttp) REVERT: H 150 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4702 (tpt170) REVERT: H 163 ASP cc_start: 0.6817 (p0) cc_final: 0.6585 (p0) REVERT: H 166 GLU cc_start: 0.8660 (mp0) cc_final: 0.8011 (mp0) REVERT: H 174 LEU cc_start: 0.8151 (mt) cc_final: 0.7864 (mt) REVERT: J 151 ASP cc_start: 0.5723 (m-30) cc_final: 0.5100 (t0) REVERT: J 178 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.4476 (pp) REVERT: J 197 GLU cc_start: 0.6424 (pp20) cc_final: 0.6178 (pp20) REVERT: K 9 ASP cc_start: 0.8709 (t0) cc_final: 0.8029 (p0) REVERT: K 154 GLN cc_start: 0.8984 (pt0) cc_final: 0.8222 (mm-40) REVERT: K 166 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7780 (tp-100) REVERT: K 189 GLU cc_start: 0.8899 (mp0) cc_final: 0.8546 (tp30) REVERT: K 251 LEU cc_start: 0.1903 (OUTLIER) cc_final: 0.1664 (tp) outliers start: 86 outliers final: 68 residues processed: 406 average time/residue: 0.1239 time to fit residues: 80.4653 Evaluate side-chains 389 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 314 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 VAL 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 531 ASN Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ILE 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 55 VAL Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 80 THR 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 30 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 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 J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR 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 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 72 optimal weight: 3.9990 chunk 250 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 371 GLN ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS H 195 ASN J 87 GLN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.096095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.079364 restraints weight = 97316.972| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 5.55 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 1.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.307 21465 Z= 0.302 Angle : 1.130 25.102 29095 Z= 0.557 Chirality : 0.055 0.488 3279 Planarity : 0.007 0.105 3679 Dihedral : 5.734 59.192 3028 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.97 % Favored : 90.60 % Rotamer: Outliers : 3.74 % Allowed : 32.44 % Favored : 63.82 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2597 helix: 0.54 (0.17), residues: 896 sheet: 0.26 (0.20), residues: 663 loop : -3.18 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 854 TYR 0.049 0.003 TYR B 8 PHE 0.064 0.004 PHE B 230 TRP 0.042 0.003 TRP A 110 HIS 0.027 0.003 HIS A 663 Details of bonding type rmsd covalent geometry : bond 0.00650 (21456) covalent geometry : angle 1.12607 (29068) hydrogen bonds : bond 0.04847 ( 972) hydrogen bonds : angle 5.60355 ( 2847) link_BETA1-4 : bond 0.01030 ( 6) link_BETA1-4 : angle 2.07115 ( 18) link_NAG-ASN : bond 0.01580 ( 3) link_NAG-ASN : angle 4.53759 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4489.53 seconds wall clock time: 77 minutes 57.72 seconds (4677.72 seconds total)