Starting phenix.real_space_refine on Sun Aug 24 08:37:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0n_35906/08_2025/8j0n_35906.cif" } resolution = 3.47 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= 0.034 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 88 5.16 5 C 11829 2.51 5 N 3152 2.21 5 O 3406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s 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: 18475 Number of models: 1 Model: "" Number of chains: 12 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: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain breaks: 1 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: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} 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: "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: 3.67, per 1000 atoms: 0.20 Number of scatterers: 18475 At special positions: 0 Unit cell: (131.89, 212.55, 113.36, 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 88 16.00 O 3406 8.00 N 3152 7.00 C 11829 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: 1.16 Conformation dependent library (CDL) restraints added in 628.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 39.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 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: 3.628A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 993 removed outlier: 3.908A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.511A pdb=" N ASP B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.199A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.828A pdb=" N ILE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.873A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.595A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.827A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.519A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.586A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.668A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.571A pdb=" N LYS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.909A pdb=" N SER B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.535A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix 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 removed outlier: 3.858A pdb=" N LYS C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.660A pdb=" N MET C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) 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: 3.843A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 187 removed outlier: 4.209A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 209 removed outlier: 3.748A pdb=" N MET C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.711A pdb=" N LEU C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.712A 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 246 through 257 removed outlier: 3.645A pdb=" N GLY C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.984A pdb=" N VAL D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 113 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.751A pdb=" N THR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 155 removed outlier: 3.562A pdb=" N PHE D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.523A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 34 removed outlier: 3.505A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.568A pdb=" N VAL E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 61 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.671A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 removed outlier: 3.931A pdb=" N VAL E 99 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.528A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.511A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.993A 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: 3.671A pdb=" N LEU F 98 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.671A pdb=" N SER G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.624A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 3.685A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 119 removed outlier: 3.997A 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 Processing helix chain 'J' and resid 133 through 140 removed outlier: 4.072A pdb=" N LEU J 137 " --> pdb=" O PRO J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.675A pdb=" N PHE J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.523A 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 44 removed outlier: 3.639A pdb=" N SER A 44 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 55 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.598A pdb=" N THR A 99 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 107 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 120 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 6.714A 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: 4.040A pdb=" N TRP A 163 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.654A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.454A 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: 3.901A pdb=" N GLY A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 236 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.809A pdb=" N ARG A 275 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 292 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 303 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 293 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 301 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 313 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 326 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: 3.505A pdb=" N GLY A 418 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 412 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.808A 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: 4.351A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 458 removed outlier: 3.932A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 545 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 558 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 547 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 633 removed outlier: 3.501A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 641 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 639 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 631 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 637 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 692 through 699 removed outlier: 5.846A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A 696 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 682 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 670 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY D 180 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR A 672 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 711 removed outlier: 7.047A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 757 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 3.705A 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: 5.080A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.578A 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: 3.849A 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: 3.779A pdb=" N ASP G 88 " --> pdb=" O PHE G 45 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE G 45 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU G 138 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.558A pdb=" N ARG G 66 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.796A 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: 6.857A pdb=" N GLY H 3 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE H 54 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS H 5 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL H 31 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS H 57 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 29 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN H 27 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE H 61 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA H 25 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 26 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY H 91 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 125 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 127 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.623A 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: 6.106A pdb=" N LYS J 70 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS J 58 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 72 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 56 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU J 55 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG J 109 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 128 " --> pdb=" O ILE J 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 156 through 162 removed outlier: 6.746A pdb=" N HIS J 149 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL J 159 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR J 147 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL J 161 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN J 145 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL J 150 " --> pdb=" O GLN J 188 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2397 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: 2.38 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1 1.04 - 1.23: 356 1.23 - 1.43: 7585 1.43 - 1.62: 10795 1.62 - 1.82: 153 Bond restraints: 18890 Sorted by residual: bond pdb=" CG PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.503 0.841 0.662 3.40e-02 8.65e+02 3.79e+02 bond pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.473 1.592 -0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" CB PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 1.492 1.797 -0.305 5.00e-02 4.00e+02 3.72e+01 bond pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " ideal model delta sigma weight residual 1.521 1.598 -0.077 1.48e-02 4.57e+03 2.73e+01 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.28e+01 ... (remaining 18885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 25522 5.29 - 10.58: 61 10.58 - 15.87: 5 15.87 - 21.17: 2 21.17 - 26.46: 1 Bond angle restraints: 25591 Sorted by residual: angle pdb=" N PRO A 582 " pdb=" CD PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 103.20 76.74 26.46 1.50e+00 4.44e-01 3.11e+02 angle pdb=" CA PRO C 69 " pdb=" N PRO C 69 " pdb=" CD PRO C 69 " ideal model delta sigma weight residual 112.00 95.66 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" CD PRO E 103 " ideal model delta sigma weight residual 112.00 97.35 14.65 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 112.00 97.77 14.23 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N PRO A 582 " pdb=" CA PRO A 582 " pdb=" CB PRO A 582 " ideal model delta sigma weight residual 103.48 94.38 9.10 1.00e+00 1.00e+00 8.28e+01 ... (remaining 25586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 10034 21.59 - 43.19: 1131 43.19 - 64.78: 195 64.78 - 86.37: 45 86.37 - 107.96: 17 Dihedral angle restraints: 11422 sinusoidal: 4720 harmonic: 6702 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 180.00 147.11 32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA MET C 151 " pdb=" C MET C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+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 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2625 0.078 - 0.157: 256 0.157 - 0.235: 1 0.235 - 0.314: 5 0.314 - 0.392: 2 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" C PRO A 582 " pdb=" CB PRO A 582 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" C PRO E 103 " pdb=" CB PRO E 103 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+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 ... (remaining 2886 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 68 " 0.110 5.00e-02 4.00e+02 1.52e-01 3.71e+01 pdb=" N PRO C 69 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 581 " -0.098 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO A 582 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 102 " 0.079 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 103 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.059 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 351 2.69 - 3.24: 16640 3.24 - 3.79: 27210 3.79 - 4.35: 33688 4.35 - 4.90: 56091 Nonbonded interactions: 133980 Sorted by model distance: nonbonded pdb=" OD1 ASP B 104 " pdb=" NE2 GLN B 108 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR H 52 " pdb=" OD2 ASP H 121 " model vdw 2.140 3.040 nonbonded pdb=" OG SER A 747 " pdb=" OD1 ASP A 749 " model vdw 2.176 3.040 nonbonded pdb=" NZ LYS H 20 " pdb=" O LEU H 183 " model vdw 2.282 3.120 nonbonded pdb=" OG SER A 787 " pdb=" N GLU A 788 " model vdw 2.292 3.120 ... (remaining 133975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.662 18899 Z= 0.240 Angle : 0.837 26.457 25618 Z= 0.464 Chirality : 0.044 0.392 2889 Planarity : 0.006 0.152 3236 Dihedral : 18.252 107.964 7094 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.23 % Favored : 91.50 % Rotamer: Outliers : 0.75 % Allowed : 28.06 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.04 (0.17), residues: 2271 helix: 1.46 (0.19), residues: 836 sheet: 0.27 (0.24), residues: 444 loop : -3.25 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 102 TYR 0.021 0.001 TYR A 305 PHE 0.019 0.001 PHE C 252 TRP 0.016 0.001 TRP A 219 HIS 0.008 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00656 (18890) covalent geometry : angle 0.83333 (25591) hydrogen bonds : bond 0.16856 ( 820) hydrogen bonds : angle 6.04411 ( 2397) link_BETA1-4 : bond 0.00671 ( 6) link_BETA1-4 : angle 1.39123 ( 18) link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 3.67123 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 448 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ILE cc_start: 0.4035 (mm) cc_final: 0.3612 (mm) REVERT: B 183 MET cc_start: 0.0394 (OUTLIER) cc_final: -0.0118 (mmt) REVERT: C 56 ILE cc_start: 0.8333 (mm) cc_final: 0.8131 (mt) REVERT: C 81 ASN cc_start: 0.4450 (m110) cc_final: 0.3680 (t0) REVERT: C 121 MET cc_start: 0.4674 (ppp) cc_final: 0.4261 (tpp) REVERT: C 232 TRP cc_start: 0.1901 (t60) cc_final: 0.1363 (t60) REVERT: E 31 MET cc_start: 0.6029 (tpt) cc_final: 0.5366 (ttt) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.1679 time to fit residues: 108.0688 Evaluate side-chains 244 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain D residue 43 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0020 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 102 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS B 193 GLN B 194 GLN C 81 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN H 199 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.102714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.084488 restraints weight = 74235.106| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.61 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3763 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18899 Z= 0.159 Angle : 0.783 12.242 25618 Z= 0.384 Chirality : 0.045 0.262 2889 Planarity : 0.006 0.105 3236 Dihedral : 7.700 67.890 2691 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.32 % Favored : 91.33 % Rotamer: Outliers : 4.14 % Allowed : 27.66 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.84 (0.17), residues: 2271 helix: 1.44 (0.18), residues: 859 sheet: 0.43 (0.23), residues: 474 loop : -3.20 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 150 TYR 0.024 0.002 TYR C 67 PHE 0.028 0.002 PHE B 230 TRP 0.020 0.002 TRP A 557 HIS 0.009 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00357 (18890) covalent geometry : angle 0.77876 (25591) hydrogen bonds : bond 0.04589 ( 820) hydrogen bonds : angle 5.12218 ( 2397) link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 2.26812 ( 18) link_NAG-ASN : bond 0.00235 ( 3) link_NAG-ASN : angle 3.00131 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.4413 (OUTLIER) cc_final: 0.4107 (t) REVERT: A 174 HIS cc_start: 0.8740 (t-170) cc_final: 0.8510 (t70) REVERT: A 375 ILE cc_start: 0.7333 (mt) cc_final: 0.6252 (mt) REVERT: A 395 LEU cc_start: 0.6599 (mt) cc_final: 0.6323 (mp) REVERT: A 907 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 919 MET cc_start: 0.6849 (mmm) cc_final: 0.5161 (tpp) REVERT: B 19 MET cc_start: 0.4221 (mtp) cc_final: 0.3793 (mtp) REVERT: B 32 GLN cc_start: 0.7263 (tp40) cc_final: 0.6246 (pp30) REVERT: B 39 GLU cc_start: 0.4401 (OUTLIER) cc_final: 0.4145 (tp30) REVERT: B 64 LEU cc_start: 0.2578 (OUTLIER) cc_final: 0.2239 (tp) REVERT: B 182 MET cc_start: 0.2247 (mtp) cc_final: 0.2028 (mtp) REVERT: B 183 MET cc_start: 0.1216 (OUTLIER) cc_final: 0.0531 (mmt) REVERT: C 36 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.4938 (mt) REVERT: C 77 LYS cc_start: 0.6648 (mmtp) cc_final: 0.5797 (mmtm) REVERT: C 121 MET cc_start: 0.4662 (ppp) cc_final: 0.4198 (tpp) REVERT: C 216 LYS cc_start: 0.9285 (ptmt) cc_final: 0.9046 (ptpp) REVERT: C 232 TRP cc_start: 0.4267 (t60) cc_final: 0.2450 (t60) REVERT: D 87 MET cc_start: 0.4510 (mtm) cc_final: 0.4149 (mtm) REVERT: E 31 MET cc_start: 0.5313 (tpt) cc_final: 0.5093 (ttt) REVERT: F 107 VAL cc_start: 0.6210 (p) cc_final: 0.6009 (p) REVERT: H 110 LYS cc_start: 0.6012 (tptp) cc_final: 0.5092 (pttp) REVERT: H 163 ASP cc_start: 0.8152 (t0) cc_final: 0.7622 (t0) REVERT: J 70 LYS cc_start: 0.6328 (tmtt) cc_final: 0.6094 (tppt) REVERT: J 77 ASN cc_start: 0.6516 (t0) cc_final: 0.6270 (t0) outliers start: 83 outliers final: 23 residues processed: 335 average time/residue: 0.1307 time to fit residues: 65.3788 Evaluate side-chains 238 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 108 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 189 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 262 GLN A 491 GLN A 559 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A 832 GLN B 188 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS D 140 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN H 199 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.101136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.083711 restraints weight = 76658.337| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 5.63 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4428 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18899 Z= 0.214 Angle : 0.851 14.381 25618 Z= 0.418 Chirality : 0.048 0.323 2889 Planarity : 0.006 0.113 3236 Dihedral : 5.685 59.644 2689 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.23 % Favored : 91.41 % Rotamer: Outliers : 4.99 % Allowed : 26.81 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.17), residues: 2271 helix: 1.16 (0.18), residues: 857 sheet: 0.30 (0.23), residues: 466 loop : -3.07 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 126 TYR 0.022 0.002 TYR B 171 PHE 0.027 0.003 PHE A 671 TRP 0.028 0.003 TRP B 158 HIS 0.022 0.002 HIS A 751 Details of bonding type rmsd covalent geometry : bond 0.00474 (18890) covalent geometry : angle 0.84657 (25591) hydrogen bonds : bond 0.04472 ( 820) hydrogen bonds : angle 5.33278 ( 2397) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 2.64960 ( 18) link_NAG-ASN : bond 0.00576 ( 3) link_NAG-ASN : angle 2.79819 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 287 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8655 (t-170) cc_final: 0.8408 (t-90) REVERT: A 292 PHE cc_start: 0.6883 (m-80) cc_final: 0.6615 (m-10) REVERT: A 375 ILE cc_start: 0.7701 (mt) cc_final: 0.7171 (mt) REVERT: A 686 LEU cc_start: -0.1435 (OUTLIER) cc_final: -0.1814 (mt) REVERT: A 740 LEU cc_start: -0.1181 (OUTLIER) cc_final: -0.1408 (mm) REVERT: B 19 MET cc_start: 0.4862 (mtp) cc_final: 0.4364 (mtp) REVERT: B 182 MET cc_start: 0.2940 (mtp) cc_final: 0.2599 (mmm) REVERT: C 36 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.4985 (mt) REVERT: C 74 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 77 LYS cc_start: 0.6993 (mmtp) cc_final: 0.5990 (mmtt) REVERT: C 121 MET cc_start: 0.5640 (ppp) cc_final: 0.4964 (tpp) REVERT: C 137 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.6590 (p) REVERT: C 232 TRP cc_start: 0.4754 (t60) cc_final: 0.4444 (t60) REVERT: E 31 MET cc_start: 0.5899 (tpt) cc_final: 0.5443 (ttt) REVERT: G 79 LYS cc_start: 0.4116 (OUTLIER) cc_final: 0.3896 (pttp) REVERT: H 126 MET cc_start: 0.7773 (tmm) cc_final: 0.7495 (tmm) REVERT: J 55 LEU cc_start: 0.3797 (pt) cc_final: 0.3141 (tp) REVERT: J 77 ASN cc_start: 0.7515 (t0) cc_final: 0.7229 (t0) REVERT: J 192 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7383 (t) outliers start: 100 outliers final: 48 residues processed: 372 average time/residue: 0.1310 time to fit residues: 73.5755 Evaluate side-chains 289 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 27 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 771 HIS ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN B 167 ASN B 238 HIS ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.082838 restraints weight = 79465.491| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 5.70 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18899 Z= 0.180 Angle : 0.782 12.657 25618 Z= 0.380 Chirality : 0.045 0.298 2889 Planarity : 0.006 0.064 3236 Dihedral : 5.046 59.233 2686 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.23 % Favored : 91.37 % Rotamer: Outliers : 4.84 % Allowed : 27.96 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.84 (0.17), residues: 2271 helix: 1.32 (0.18), residues: 854 sheet: 0.30 (0.23), residues: 475 loop : -2.95 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 445 TYR 0.036 0.002 TYR B 8 PHE 0.022 0.002 PHE B 230 TRP 0.018 0.002 TRP A 110 HIS 0.009 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00404 (18890) covalent geometry : angle 0.77953 (25591) hydrogen bonds : bond 0.03932 ( 820) hydrogen bonds : angle 5.11851 ( 2397) link_BETA1-4 : bond 0.00367 ( 6) link_BETA1-4 : angle 1.94545 ( 18) link_NAG-ASN : bond 0.00500 ( 3) link_NAG-ASN : angle 2.72986 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 272 time to evaluate : 0.705 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: A 105 ARG cc_start: 0.6317 (mmm160) cc_final: 0.6031 (mmm160) REVERT: A 131 LEU cc_start: 0.7399 (mt) cc_final: 0.6812 (tt) REVERT: A 375 ILE cc_start: 0.7528 (mt) cc_final: 0.7313 (mt) REVERT: A 434 GLN cc_start: 0.4329 (OUTLIER) cc_final: 0.3081 (pm20) REVERT: A 848 GLU cc_start: 0.6665 (pp20) cc_final: 0.5845 (pm20) REVERT: B 8 TYR cc_start: 0.7216 (m-10) cc_final: 0.6995 (m-80) REVERT: C 74 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 121 MET cc_start: 0.5656 (ppp) cc_final: 0.4923 (tpp) REVERT: C 137 THR cc_start: 0.7146 (m) cc_final: 0.6881 (p) REVERT: C 232 TRP cc_start: 0.4859 (t60) cc_final: 0.4350 (t60) REVERT: D 100 MET cc_start: 0.7712 (ppp) cc_final: 0.7161 (ppp) REVERT: D 101 MET cc_start: 0.7614 (mtt) cc_final: 0.6797 (ptp) REVERT: D 105 MET cc_start: 0.7319 (mmm) cc_final: 0.7044 (mpp) REVERT: D 140 ASN cc_start: 0.3728 (OUTLIER) cc_final: 0.3322 (t0) REVERT: E 31 MET cc_start: 0.5764 (tpt) cc_final: 0.5398 (ttt) REVERT: G 124 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.5877 (t0) REVERT: G 140 MET cc_start: 0.4348 (tpt) cc_final: 0.3706 (tpt) REVERT: H 110 LYS cc_start: 0.6712 (tptp) cc_final: 0.5914 (pttt) REVERT: H 126 MET cc_start: 0.8193 (tmm) cc_final: 0.7787 (tmm) REVERT: H 166 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7039 (tp30) REVERT: H 209 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3125 (mt) REVERT: J 55 LEU cc_start: 0.3811 (pt) cc_final: 0.3553 (tp) REVERT: J 77 ASN cc_start: 0.7661 (t0) cc_final: 0.7068 (t0) REVERT: J 80 ASP cc_start: 0.5554 (m-30) cc_final: 0.5127 (m-30) REVERT: J 151 ASP cc_start: 0.4863 (m-30) cc_final: 0.3760 (t0) outliers start: 97 outliers final: 47 residues processed: 348 average time/residue: 0.1330 time to fit residues: 70.7657 Evaluate side-chains 295 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 142 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 F residue 43 ILE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 68 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 216 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN J 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.100581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.083777 restraints weight = 78334.104| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 5.66 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18899 Z= 0.158 Angle : 0.769 12.903 25618 Z= 0.371 Chirality : 0.044 0.296 2889 Planarity : 0.005 0.063 3236 Dihedral : 4.978 59.704 2686 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.01 % Favored : 91.59 % Rotamer: Outliers : 4.59 % Allowed : 28.81 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2271 helix: 1.25 (0.18), residues: 851 sheet: 0.41 (0.24), residues: 465 loop : -2.94 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 57 TYR 0.032 0.002 TYR B 66 PHE 0.033 0.002 PHE B 230 TRP 0.017 0.002 TRP C 15 HIS 0.018 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00351 (18890) covalent geometry : angle 0.76661 (25591) hydrogen bonds : bond 0.03974 ( 820) hydrogen bonds : angle 5.05418 ( 2397) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 1.68652 ( 18) link_NAG-ASN : bond 0.00472 ( 3) link_NAG-ASN : angle 2.72958 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 276 time to evaluate : 0.719 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 105 ARG cc_start: 0.6471 (mmm160) cc_final: 0.6100 (mmm160) REVERT: A 117 LEU cc_start: 0.6474 (mt) cc_final: 0.6202 (mt) REVERT: A 336 MET cc_start: 0.6660 (mmm) cc_final: 0.6421 (mmm) REVERT: A 632 MET cc_start: 0.4750 (mmt) cc_final: 0.4528 (tpp) REVERT: A 686 LEU cc_start: -0.0951 (OUTLIER) cc_final: -0.1470 (mt) REVERT: A 740 LEU cc_start: -0.0351 (OUTLIER) cc_final: -0.0632 (mm) REVERT: A 749 ASP cc_start: 0.7392 (p0) cc_final: 0.6998 (p0) REVERT: B 8 TYR cc_start: 0.7257 (m-10) cc_final: 0.6982 (m-80) REVERT: C 137 THR cc_start: 0.7067 (m) cc_final: 0.6858 (p) REVERT: C 172 TYR cc_start: 0.3662 (t80) cc_final: 0.3435 (t80) REVERT: C 232 TRP cc_start: 0.5104 (t60) cc_final: 0.4698 (t60) REVERT: E 31 MET cc_start: 0.5964 (tpt) cc_final: 0.5394 (ttt) REVERT: E 66 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.4130 (mm-30) REVERT: E 67 PHE cc_start: 0.3554 (m-10) cc_final: 0.3160 (m-10) REVERT: F 84 LEU cc_start: 0.4755 (mp) cc_final: 0.4458 (mm) REVERT: F 85 PHE cc_start: 0.0354 (OUTLIER) cc_final: 0.0068 (t80) REVERT: H 110 LYS cc_start: 0.6757 (tptp) cc_final: 0.5912 (pttt) REVERT: H 126 MET cc_start: 0.8199 (tmm) cc_final: 0.7663 (tmm) REVERT: H 166 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7272 (tp30) REVERT: H 209 LEU cc_start: 0.3699 (OUTLIER) cc_final: 0.3338 (mm) REVERT: J 77 ASN cc_start: 0.7757 (t0) cc_final: 0.7129 (t0) outliers start: 92 outliers final: 53 residues processed: 348 average time/residue: 0.1425 time to fit residues: 75.9882 Evaluate side-chains 296 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 817 TYR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 109 optimal weight: 5.9990 chunk 221 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.100286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.083364 restraints weight = 79142.087| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 5.70 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5027 moved from start: 0.8644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18899 Z= 0.142 Angle : 0.784 14.388 25618 Z= 0.370 Chirality : 0.045 0.342 2889 Planarity : 0.005 0.081 3236 Dihedral : 4.879 59.544 2686 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.71 % Favored : 91.90 % Rotamer: Outliers : 4.14 % Allowed : 30.35 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.17), residues: 2271 helix: 1.30 (0.18), residues: 852 sheet: 0.48 (0.24), residues: 457 loop : -2.92 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.033 0.002 TYR B 66 PHE 0.034 0.002 PHE B 230 TRP 0.018 0.001 TRP H 197 HIS 0.014 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00310 (18890) covalent geometry : angle 0.78163 (25591) hydrogen bonds : bond 0.03622 ( 820) hydrogen bonds : angle 4.92666 ( 2397) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 1.61511 ( 18) link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 2.54965 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.723 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: A 105 ARG cc_start: 0.6485 (mmm160) cc_final: 0.6212 (mmm160) REVERT: A 177 MET cc_start: 0.7096 (mtt) cc_final: 0.6154 (mtt) REVERT: A 209 ILE cc_start: 0.8386 (mt) cc_final: 0.8182 (tp) REVERT: A 336 MET cc_start: 0.6864 (mmm) cc_final: 0.6626 (mmm) REVERT: A 427 ASP cc_start: -0.0202 (OUTLIER) cc_final: -0.2565 (t0) REVERT: A 434 GLN cc_start: 0.5122 (OUTLIER) cc_final: 0.3519 (pm20) REVERT: A 505 MET cc_start: 0.7519 (mmp) cc_final: 0.7197 (mmp) REVERT: A 536 MET cc_start: 0.4393 (ppp) cc_final: 0.4049 (ppp) REVERT: A 632 MET cc_start: 0.4554 (mmt) cc_final: 0.4321 (tpp) REVERT: A 686 LEU cc_start: -0.1213 (OUTLIER) cc_final: -0.1582 (mt) REVERT: A 898 TYR cc_start: 0.5574 (t80) cc_final: 0.5266 (t80) REVERT: B 8 TYR cc_start: 0.7303 (m-10) cc_final: 0.7049 (m-80) REVERT: C 51 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8677 (p0) REVERT: C 74 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 77 LYS cc_start: 0.7079 (mmtp) cc_final: 0.6201 (mmtm) REVERT: C 121 MET cc_start: 0.6230 (ttt) cc_final: 0.4981 (tpp) REVERT: C 137 THR cc_start: 0.7218 (m) cc_final: 0.6962 (p) REVERT: C 232 TRP cc_start: 0.5195 (t60) cc_final: 0.4719 (t60) REVERT: D 100 MET cc_start: 0.7390 (ppp) cc_final: 0.7023 (ppp) REVERT: D 101 MET cc_start: 0.7340 (mtt) cc_final: 0.6718 (ptp) REVERT: D 105 MET cc_start: 0.7200 (mpp) cc_final: 0.6971 (mpp) REVERT: D 174 MET cc_start: 0.5294 (pmm) cc_final: 0.4635 (pmm) REVERT: E 31 MET cc_start: 0.6121 (tpt) cc_final: 0.5615 (ttt) REVERT: F 84 LEU cc_start: 0.5033 (mp) cc_final: 0.4758 (mm) REVERT: F 85 PHE cc_start: 0.0400 (OUTLIER) cc_final: 0.0139 (t80) REVERT: G 124 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.6969 (t0) REVERT: H 14 MET cc_start: 0.6772 (tmm) cc_final: 0.6559 (tmm) REVERT: H 110 LYS cc_start: 0.6782 (tptp) cc_final: 0.5655 (ttpt) REVERT: H 209 LEU cc_start: 0.3545 (OUTLIER) cc_final: 0.3005 (mt) REVERT: J 77 ASN cc_start: 0.7811 (t0) cc_final: 0.7532 (t0) outliers start: 83 outliers final: 46 residues processed: 333 average time/residue: 0.1360 time to fit residues: 70.3845 Evaluate side-chains 291 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 817 TYR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 149 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 95 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 169 HIS C 202 GLN D 140 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** 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 = 0.4164 r_free = 0.4164 target = 0.099126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.082213 restraints weight = 81464.323| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 5.86 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.9731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18899 Z= 0.177 Angle : 0.807 12.652 25618 Z= 0.395 Chirality : 0.047 0.590 2889 Planarity : 0.006 0.091 3236 Dihedral : 5.047 59.288 2686 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.88 % Favored : 91.72 % Rotamer: Outliers : 4.04 % Allowed : 30.25 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.99 (0.17), residues: 2271 helix: 1.15 (0.18), residues: 860 sheet: 0.27 (0.23), residues: 462 loop : -3.01 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 16 TYR 0.020 0.002 TYR E 30 PHE 0.059 0.002 PHE H 61 TRP 0.020 0.002 TRP H 197 HIS 0.014 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00384 (18890) covalent geometry : angle 0.80492 (25591) hydrogen bonds : bond 0.03924 ( 820) hydrogen bonds : angle 5.00166 ( 2397) link_BETA1-4 : bond 0.00621 ( 6) link_BETA1-4 : angle 1.57481 ( 18) link_NAG-ASN : bond 0.00591 ( 3) link_NAG-ASN : angle 2.86689 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 287 time to evaluate : 0.719 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 336 MET cc_start: 0.6882 (mmm) cc_final: 0.6658 (mmm) REVERT: A 434 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5593 (tp-100) REVERT: A 536 MET cc_start: 0.5025 (ppp) cc_final: 0.4715 (ppp) REVERT: A 632 MET cc_start: 0.4542 (mmt) cc_final: 0.4320 (tpp) REVERT: A 686 LEU cc_start: -0.0977 (OUTLIER) cc_final: -0.1405 (mt) REVERT: A 757 ILE cc_start: 0.2677 (OUTLIER) cc_final: 0.2020 (mm) REVERT: A 898 TYR cc_start: 0.5852 (t80) cc_final: 0.5516 (t80) REVERT: B 8 TYR cc_start: 0.7528 (m-10) cc_final: 0.7286 (m-80) REVERT: B 55 ILE cc_start: 0.6541 (mm) cc_final: 0.6174 (mm) REVERT: B 215 PHE cc_start: 0.1113 (OUTLIER) cc_final: 0.0694 (t80) REVERT: C 51 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8736 (p0) REVERT: C 74 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8788 (tp) REVERT: C 77 LYS cc_start: 0.7239 (mmtp) cc_final: 0.6395 (mmtm) REVERT: C 121 MET cc_start: 0.6595 (ttt) cc_final: 0.5193 (tpp) REVERT: C 137 THR cc_start: 0.7534 (m) cc_final: 0.7187 (p) REVERT: C 151 MET cc_start: 0.7232 (mmt) cc_final: 0.6952 (mtm) REVERT: C 232 TRP cc_start: 0.5504 (t60) cc_final: 0.4979 (t60) REVERT: D 101 MET cc_start: 0.7678 (mtt) cc_final: 0.7446 (ptp) REVERT: D 104 MET cc_start: 0.7255 (tpp) cc_final: 0.6688 (ptp) REVERT: E 31 MET cc_start: 0.6237 (tpt) cc_final: 0.5635 (ttt) REVERT: F 84 LEU cc_start: 0.5356 (mp) cc_final: 0.5048 (mm) REVERT: H 110 LYS cc_start: 0.6841 (tptp) cc_final: 0.6172 (pttt) REVERT: H 170 ILE cc_start: 0.6030 (tt) cc_final: 0.5664 (tp) REVERT: J 77 ASN cc_start: 0.8034 (t0) cc_final: 0.7651 (t0) outliers start: 81 outliers final: 53 residues processed: 350 average time/residue: 0.1377 time to fit residues: 74.6256 Evaluate side-chains 311 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 218 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.099083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.082351 restraints weight = 81368.003| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.87 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 1.0114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18899 Z= 0.141 Angle : 0.811 13.203 25618 Z= 0.385 Chirality : 0.046 0.371 2889 Planarity : 0.005 0.061 3236 Dihedral : 4.921 59.485 2686 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.66 % Favored : 91.94 % Rotamer: Outliers : 3.10 % Allowed : 32.15 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.17), residues: 2271 helix: 1.16 (0.18), residues: 862 sheet: 0.30 (0.23), residues: 473 loop : -2.98 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 180 TYR 0.029 0.001 TYR E 30 PHE 0.042 0.002 PHE H 61 TRP 0.018 0.001 TRP A 254 HIS 0.016 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00316 (18890) covalent geometry : angle 0.80838 (25591) hydrogen bonds : bond 0.03684 ( 820) hydrogen bonds : angle 4.94943 ( 2397) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 1.60022 ( 18) link_NAG-ASN : bond 0.00498 ( 3) link_NAG-ASN : angle 2.68272 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ILE cc_start: 0.8418 (mt) cc_final: 0.8029 (tp) REVERT: A 336 MET cc_start: 0.7081 (mmm) cc_final: 0.6805 (mmm) REVERT: A 434 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5520 (tp-100) REVERT: A 457 MET cc_start: 0.4726 (OUTLIER) cc_final: 0.4252 (mmm) REVERT: A 536 MET cc_start: 0.5057 (ppp) cc_final: 0.4851 (ppp) REVERT: A 898 TYR cc_start: 0.5739 (t80) cc_final: 0.5394 (t80) REVERT: B 215 PHE cc_start: 0.1607 (OUTLIER) cc_final: 0.1092 (t80) REVERT: C 6 LEU cc_start: 0.7354 (tp) cc_final: 0.7029 (tp) REVERT: C 51 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8789 (p0) REVERT: C 74 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8812 (tp) REVERT: C 77 LYS cc_start: 0.7235 (mmtp) cc_final: 0.6398 (mmtm) REVERT: C 121 MET cc_start: 0.6599 (ttt) cc_final: 0.5382 (tpp) REVERT: C 137 THR cc_start: 0.7441 (m) cc_final: 0.7144 (p) REVERT: C 147 ARG cc_start: 0.3982 (mtt180) cc_final: 0.3248 (mtm180) REVERT: C 151 MET cc_start: 0.7248 (mmt) cc_final: 0.6996 (mtm) REVERT: C 232 TRP cc_start: 0.5595 (t60) cc_final: 0.5003 (t60) REVERT: D 50 LYS cc_start: 0.8835 (pttp) cc_final: 0.8459 (ptpp) REVERT: D 104 MET cc_start: 0.7246 (tpp) cc_final: 0.6736 (ptp) REVERT: E 31 MET cc_start: 0.6171 (tpt) cc_final: 0.5582 (ttt) REVERT: F 84 LEU cc_start: 0.5497 (mp) cc_final: 0.5235 (mm) REVERT: G 124 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8050 (t0) REVERT: H 110 LYS cc_start: 0.6860 (tptp) cc_final: 0.6145 (pttt) REVERT: H 170 ILE cc_start: 0.6277 (tt) cc_final: 0.5995 (tp) REVERT: J 77 ASN cc_start: 0.7929 (t0) cc_final: 0.7467 (t0) REVERT: J 185 VAL cc_start: 0.8615 (t) cc_final: 0.8344 (m) outliers start: 62 outliers final: 44 residues processed: 311 average time/residue: 0.1318 time to fit residues: 64.8722 Evaluate side-chains 301 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 154 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 61 ASN A 371 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 238 HIS ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN H 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.097400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.080423 restraints weight = 83022.496| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 5.98 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 1.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18899 Z= 0.194 Angle : 0.889 16.736 25618 Z= 0.439 Chirality : 0.049 0.441 2889 Planarity : 0.006 0.068 3236 Dihedral : 5.236 59.289 2686 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.79 % Favored : 91.81 % Rotamer: Outliers : 3.49 % Allowed : 32.40 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.13 (0.17), residues: 2271 helix: 1.04 (0.18), residues: 858 sheet: 0.07 (0.23), residues: 474 loop : -3.04 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 105 TYR 0.042 0.002 TYR B 66 PHE 0.087 0.003 PHE H 61 TRP 0.019 0.002 TRP A 254 HIS 0.025 0.002 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00411 (18890) covalent geometry : angle 0.88689 (25591) hydrogen bonds : bond 0.04052 ( 820) hydrogen bonds : angle 5.18750 ( 2397) link_BETA1-4 : bond 0.00528 ( 6) link_BETA1-4 : angle 1.59458 ( 18) link_NAG-ASN : bond 0.00948 ( 3) link_NAG-ASN : angle 3.21449 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.742 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: A 34 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6723 (tp40) REVERT: A 35 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: A 177 MET cc_start: 0.7005 (mtt) cc_final: 0.6225 (mtt) REVERT: A 336 MET cc_start: 0.7221 (mmm) cc_final: 0.6986 (mmm) REVERT: A 531 ASN cc_start: 0.7614 (p0) cc_final: 0.7235 (p0) REVERT: A 535 MET cc_start: 0.5140 (ttm) cc_final: 0.4502 (ttt) REVERT: A 536 MET cc_start: 0.6119 (ppp) cc_final: 0.5780 (ptm) REVERT: A 632 MET cc_start: 0.4273 (mmt) cc_final: 0.3896 (mmm) REVERT: A 660 ARG cc_start: 0.9071 (ptt-90) cc_final: 0.8818 (ptt-90) REVERT: A 898 TYR cc_start: 0.5500 (t80) cc_final: 0.5235 (t80) REVERT: A 992 TRP cc_start: 0.4913 (m100) cc_final: 0.3409 (t-100) REVERT: B 215 PHE cc_start: 0.2687 (OUTLIER) cc_final: 0.2036 (t80) REVERT: C 51 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8679 (p0) REVERT: C 74 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8783 (tp) REVERT: C 77 LYS cc_start: 0.7448 (mmtp) cc_final: 0.6535 (mmtm) REVERT: C 121 MET cc_start: 0.6840 (ttt) cc_final: 0.5813 (tpp) REVERT: C 137 THR cc_start: 0.7581 (m) cc_final: 0.7304 (p) REVERT: C 232 TRP cc_start: 0.6058 (t60) cc_final: 0.5743 (t60) REVERT: D 50 LYS cc_start: 0.8786 (pttp) cc_final: 0.8430 (ptpp) REVERT: D 104 MET cc_start: 0.7063 (tpp) cc_final: 0.6496 (ptp) REVERT: D 120 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3321 (m-80) REVERT: E 31 MET cc_start: 0.6460 (tpt) cc_final: 0.5883 (ttt) REVERT: E 88 PRO cc_start: 0.6125 (Cg_exo) cc_final: 0.5337 (Cg_endo) REVERT: G 124 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.7727 (t0) REVERT: H 9 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6362 (pp30) REVERT: H 61 PHE cc_start: 0.7815 (t80) cc_final: 0.7546 (t80) REVERT: H 111 VAL cc_start: 0.6430 (m) cc_final: 0.6137 (m) REVERT: H 203 ASN cc_start: 0.8576 (m-40) cc_final: 0.8347 (m110) REVERT: J 77 ASN cc_start: 0.8190 (t0) cc_final: 0.7799 (t0) REVERT: J 185 VAL cc_start: 0.8549 (t) cc_final: 0.8306 (t) outliers start: 70 outliers final: 48 residues processed: 345 average time/residue: 0.1226 time to fit residues: 67.2772 Evaluate side-chains 316 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** 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 = 0.4136 r_free = 0.4136 target = 0.097567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.080366 restraints weight = 83265.772| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 6.07 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 1.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18899 Z= 0.165 Angle : 0.872 15.414 25618 Z= 0.415 Chirality : 0.046 0.333 2889 Planarity : 0.006 0.083 3236 Dihedral : 5.126 59.980 2686 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.66 % Favored : 91.99 % Rotamer: Outliers : 2.60 % Allowed : 34.05 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.17), residues: 2271 helix: 1.07 (0.18), residues: 852 sheet: 0.24 (0.23), residues: 479 loop : -3.00 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 121 TYR 0.034 0.002 TYR A 36 PHE 0.030 0.002 PHE B 215 TRP 0.024 0.001 TRP H 197 HIS 0.011 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00371 (18890) covalent geometry : angle 0.86986 (25591) hydrogen bonds : bond 0.03895 ( 820) hydrogen bonds : angle 5.08965 ( 2397) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 1.55248 ( 18) link_NAG-ASN : bond 0.00726 ( 3) link_NAG-ASN : angle 2.96675 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 0.653 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: A 35 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: A 177 MET cc_start: 0.7127 (mtt) cc_final: 0.6238 (mtt) REVERT: A 336 MET cc_start: 0.7398 (mmm) cc_final: 0.7105 (mmm) REVERT: A 531 ASN cc_start: 0.7716 (p0) cc_final: 0.7292 (p0) REVERT: A 536 MET cc_start: 0.6602 (ppp) cc_final: 0.6337 (ptm) REVERT: A 632 MET cc_start: 0.4439 (mmt) cc_final: 0.3949 (mmm) REVERT: A 678 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: A 898 TYR cc_start: 0.5503 (t80) cc_final: 0.5227 (t80) REVERT: B 115 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: B 215 PHE cc_start: 0.2930 (OUTLIER) cc_final: 0.2025 (t80) REVERT: B 234 MET cc_start: 0.7456 (ptt) cc_final: 0.7243 (ptm) REVERT: C 51 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8813 (p0) REVERT: C 74 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8772 (tp) REVERT: C 77 LYS cc_start: 0.7538 (mmtp) cc_final: 0.6628 (mmtm) REVERT: C 121 MET cc_start: 0.7112 (ttt) cc_final: 0.6144 (tpp) REVERT: C 137 THR cc_start: 0.7946 (m) cc_final: 0.7660 (p) REVERT: C 232 TRP cc_start: 0.6272 (t60) cc_final: 0.5953 (t60) REVERT: D 50 LYS cc_start: 0.8829 (pttp) cc_final: 0.8471 (ptpp) REVERT: D 120 PHE cc_start: 0.4164 (OUTLIER) cc_final: 0.3349 (m-80) REVERT: G 124 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8115 (t0) REVERT: H 14 MET cc_start: 0.7761 (tmm) cc_final: 0.7279 (tmm) REVERT: H 111 VAL cc_start: 0.6404 (m) cc_final: 0.6191 (m) REVERT: H 170 ILE cc_start: 0.7384 (tt) cc_final: 0.7043 (tp) REVERT: H 203 ASN cc_start: 0.8616 (m-40) cc_final: 0.8074 (m110) REVERT: J 77 ASN cc_start: 0.8265 (t0) cc_final: 0.7782 (t0) REVERT: J 80 ASP cc_start: 0.5774 (m-30) cc_final: 0.5447 (m-30) outliers start: 52 outliers final: 39 residues processed: 322 average time/residue: 0.1170 time to fit residues: 60.7040 Evaluate side-chains 319 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 210 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN H 9 GLN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.097353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080104 restraints weight = 83543.995| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 6.12 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 1.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18899 Z= 0.155 Angle : 0.872 14.184 25618 Z= 0.415 Chirality : 0.046 0.339 2889 Planarity : 0.005 0.059 3236 Dihedral : 5.060 59.869 2686 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.57 % Favored : 92.07 % Rotamer: Outliers : 2.70 % Allowed : 34.60 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.17), residues: 2271 helix: 1.08 (0.18), residues: 850 sheet: 0.41 (0.24), residues: 462 loop : -3.00 (0.17), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 660 TYR 0.022 0.002 TYR B 66 PHE 0.035 0.002 PHE B 230 TRP 0.020 0.001 TRP A 992 HIS 0.015 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00349 (18890) covalent geometry : angle 0.87016 (25591) hydrogen bonds : bond 0.03753 ( 820) hydrogen bonds : angle 5.02800 ( 2397) link_BETA1-4 : bond 0.00392 ( 6) link_BETA1-4 : angle 1.56632 ( 18) link_NAG-ASN : bond 0.00594 ( 3) link_NAG-ASN : angle 2.83665 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.06 seconds wall clock time: 66 minutes 41.18 seconds (4001.18 seconds total)