Starting phenix.real_space_refine on Mon Jun 16 08:58:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0n_35906/06_2025/8j0n_35906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0n_35906/06_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_35906/06_2025/8j0n_35906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0n_35906/06_2025/8j0n_35906.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0n_35906/06_2025/8j0n_35906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0n_35906/06_2025/8j0n_35906.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.44, per 1000 atoms: 0.62 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: 4.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.00 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: 7.08 Time building geometry restraints manager: 5.85 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: 3.130 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 43.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.840 ------------------------------------------------------------------------------- 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 : 9.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (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 TRP 0.016 0.001 TRP A 219 HIS 0.008 0.001 HIS A 306 PHE 0.019 0.001 PHE C 252 TYR 0.021 0.001 TYR A 305 ARG 0.010 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 3.67123 ( 9) link_BETA1-4 : bond 0.00671 ( 6) link_BETA1-4 : angle 1.39123 ( 18) hydrogen bonds : bond 0.16856 ( 820) hydrogen bonds : angle 6.04411 ( 2397) covalent geometry : bond 0.00656 (18890) covalent geometry : angle 0.83333 (25591) *********************** 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 : 1.919 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: B 33 ILE cc_start: 0.4595 (mt) cc_final: 0.4198 (mt) REVERT: B 107 ILE cc_start: 0.4035 (mm) cc_final: 0.3611 (mm) REVERT: B 183 MET cc_start: 0.0394 (OUTLIER) cc_final: -0.0118 (mmt) REVERT: C 81 ASN cc_start: 0.4450 (m110) cc_final: 0.3554 (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: 0.1362 (t60) REVERT: E 31 MET cc_start: 0.6029 (tpt) cc_final: 0.5370 (ttt) REVERT: H 110 LYS cc_start: 0.5931 (mttt) cc_final: 0.5726 (tptp) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.4037 time to fit residues: 257.7494 Evaluate side-chains 243 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 190 optimal weight: 8.9990 chunk 171 optimal weight: 0.0870 chunk 95 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 188 ASN B 193 GLN B 194 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.102021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.083796 restraints weight = 74114.627| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 5.61 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3887 moved from start: 0.3901 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= 0.178 Angle : 0.781 12.254 25618 Z= 0.385 Chirality : 0.045 0.254 2889 Planarity : 0.006 0.102 3236 Dihedral : 7.460 65.444 2691 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.23 % Favored : 91.46 % Rotamer: Outliers : 4.79 % Allowed : 27.86 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2271 helix: 1.46 (0.18), residues: 862 sheet: 0.34 (0.24), residues: 458 loop : -3.18 (0.16), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 557 HIS 0.010 0.002 HIS E 62 PHE 0.028 0.002 PHE B 230 TYR 0.024 0.002 TYR C 67 ARG 0.009 0.001 ARG A 891 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 3) link_NAG-ASN : angle 3.02095 ( 9) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 2.25444 ( 18) hydrogen bonds : bond 0.04550 ( 820) hydrogen bonds : angle 5.11871 ( 2397) covalent geometry : bond 0.00404 (18890) covalent geometry : angle 0.77672 (25591) *********************** 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 361 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 265 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.4523 (OUTLIER) cc_final: 0.4270 (t) REVERT: A 90 MET cc_start: 0.7622 (tmm) cc_final: 0.7197 (tmm) REVERT: A 174 HIS cc_start: 0.8755 (t-170) cc_final: 0.8537 (t70) REVERT: A 177 MET cc_start: 0.6293 (mmm) cc_final: 0.5856 (mtt) REVERT: A 294 HIS cc_start: 0.6416 (t-170) cc_final: 0.5800 (t-170) REVERT: A 375 ILE cc_start: 0.7436 (mt) cc_final: 0.6426 (mt) REVERT: A 847 MET cc_start: 0.1531 (mmt) cc_final: -0.0160 (mtm) REVERT: A 907 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 32 GLN cc_start: 0.7184 (pp30) cc_final: 0.6984 (pp30) REVERT: B 39 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.4327 (tp30) REVERT: B 64 LEU cc_start: 0.2859 (OUTLIER) cc_final: 0.2484 (tp) REVERT: B 182 MET cc_start: 0.2580 (mtp) cc_final: 0.2333 (mtp) REVERT: B 183 MET cc_start: 0.1956 (OUTLIER) cc_final: 0.1205 (mmt) REVERT: B 226 MET cc_start: 0.2060 (tpt) cc_final: 0.1819 (tpt) REVERT: C 36 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.4946 (mt) REVERT: C 121 MET cc_start: 0.4831 (ppp) cc_final: 0.4300 (tpp) REVERT: C 216 LYS cc_start: 0.9278 (ptmt) cc_final: 0.9033 (ptpp) REVERT: C 232 TRP cc_start: 0.4454 (t60) cc_final: 0.2819 (t60) REVERT: E 15 PHE cc_start: 0.3413 (OUTLIER) cc_final: 0.2969 (m-10) REVERT: E 31 MET cc_start: 0.5254 (tpt) cc_final: 0.5009 (ttt) REVERT: F 107 VAL cc_start: 0.6137 (p) cc_final: 0.5929 (p) REVERT: H 110 LYS cc_start: 0.7819 (mttt) cc_final: 0.6893 (tptp) REVERT: H 166 GLU cc_start: 0.8320 (mp0) cc_final: 0.8119 (mm-30) REVERT: H 209 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.3105 (mt) REVERT: J 77 ASN cc_start: 0.6803 (t0) cc_final: 0.6585 (t0) outliers start: 96 outliers final: 23 residues processed: 348 average time/residue: 0.3112 time to fit residues: 163.0913 Evaluate side-chains 245 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 691 THR 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 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 83 SER 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 H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 107 optimal weight: 0.8980 chunk 156 optimal weight: 0.0970 chunk 200 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 836 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN D 51 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.102768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.085000 restraints weight = 73969.830| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 5.53 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4024 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18899 Z= 0.141 Angle : 0.758 11.515 25618 Z= 0.361 Chirality : 0.045 0.263 2889 Planarity : 0.005 0.065 3236 Dihedral : 5.931 58.872 2689 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.06 % Favored : 91.63 % Rotamer: Outliers : 3.44 % Allowed : 27.56 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2271 helix: 1.48 (0.18), residues: 864 sheet: 0.43 (0.23), residues: 476 loop : -3.06 (0.17), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.010 0.001 HIS E 62 PHE 0.044 0.002 PHE B 230 TYR 0.014 0.001 TYR C 67 ARG 0.008 0.001 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 3) link_NAG-ASN : angle 2.42097 ( 9) link_BETA1-4 : bond 0.00350 ( 6) link_BETA1-4 : angle 2.32550 ( 18) hydrogen bonds : bond 0.04121 ( 820) hydrogen bonds : angle 4.96757 ( 2397) covalent geometry : bond 0.00309 (18890) covalent geometry : angle 0.75495 (25591) *********************** 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 304 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5509 (mt) cc_final: 0.5101 (mt) REVERT: A 174 HIS cc_start: 0.8722 (t-170) cc_final: 0.8492 (t70) REVERT: A 177 MET cc_start: 0.6368 (mmm) cc_final: 0.6095 (mtt) REVERT: A 375 ILE cc_start: 0.7501 (mt) cc_final: 0.6838 (mt) REVERT: A 847 MET cc_start: 0.2260 (mmt) cc_final: 0.1172 (mtm) REVERT: B 32 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6894 (pp30) REVERT: B 64 LEU cc_start: 0.3443 (OUTLIER) cc_final: 0.2987 (tp) REVERT: B 181 LEU cc_start: 0.3185 (OUTLIER) cc_final: 0.2775 (mt) REVERT: B 182 MET cc_start: 0.2224 (mtp) cc_final: 0.1918 (mtt) REVERT: B 183 MET cc_start: 0.1712 (mtp) cc_final: 0.1013 (mmt) REVERT: C 36 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4986 (mt) REVERT: C 74 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8523 (tt) REVERT: C 121 MET cc_start: 0.5069 (ppp) cc_final: 0.4570 (tpp) REVERT: C 165 TRP cc_start: 0.3665 (m100) cc_final: 0.3453 (m100) REVERT: C 216 LYS cc_start: 0.9293 (ptmt) cc_final: 0.9048 (ptpp) REVERT: C 232 TRP cc_start: 0.4429 (t60) cc_final: 0.2720 (t60) REVERT: D 100 MET cc_start: 0.7785 (ppp) cc_final: 0.7369 (ppp) REVERT: E 15 PHE cc_start: 0.3669 (OUTLIER) cc_final: 0.3183 (m-10) REVERT: E 31 MET cc_start: 0.5536 (tpt) cc_final: 0.5126 (ttt) REVERT: H 110 LYS cc_start: 0.7935 (mttt) cc_final: 0.7004 (tptp) REVERT: J 70 LYS cc_start: 0.6495 (tmtt) cc_final: 0.5966 (mmmt) REVERT: J 77 ASN cc_start: 0.7002 (t0) cc_final: 0.6729 (t0) REVERT: J 192 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.7064 (t) outliers start: 69 outliers final: 30 residues processed: 295 average time/residue: 0.3341 time to fit residues: 153.1762 Evaluate side-chains 251 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL 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 691 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 15 PHE 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 G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 147 THR 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 105 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 0.0970 chunk 209 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS B 296 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.102136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.084357 restraints weight = 75319.286| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.59 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4223 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18899 Z= 0.146 Angle : 0.733 12.639 25618 Z= 0.351 Chirality : 0.044 0.288 2889 Planarity : 0.005 0.063 3236 Dihedral : 4.872 58.679 2686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.97 % Favored : 91.68 % Rotamer: Outliers : 4.29 % Allowed : 27.56 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2271 helix: 1.51 (0.18), residues: 857 sheet: 0.48 (0.23), residues: 476 loop : -2.96 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 32 HIS 0.014 0.001 HIS B 238 PHE 0.047 0.002 PHE B 230 TYR 0.013 0.001 TYR F 96 ARG 0.007 0.001 ARG A 385 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 3) link_NAG-ASN : angle 2.48198 ( 9) link_BETA1-4 : bond 0.00392 ( 6) link_BETA1-4 : angle 2.05738 ( 18) hydrogen bonds : bond 0.03817 ( 820) hydrogen bonds : angle 4.84006 ( 2397) covalent geometry : bond 0.00320 (18890) covalent geometry : angle 0.73012 (25591) *********************** 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 323 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.3860 (OUTLIER) cc_final: 0.3283 (t) REVERT: A 117 LEU cc_start: 0.6009 (mt) cc_final: 0.4500 (mt) REVERT: A 174 HIS cc_start: 0.8701 (t-170) cc_final: 0.8479 (t-90) REVERT: A 292 PHE cc_start: 0.6730 (m-80) cc_final: 0.6455 (m-10) REVERT: B 32 GLN cc_start: 0.7350 (pp30) cc_final: 0.7001 (pp30) REVERT: B 64 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3433 (tp) REVERT: B 181 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2890 (mt) REVERT: B 182 MET cc_start: 0.2779 (mtp) cc_final: 0.2172 (mtm) REVERT: B 183 MET cc_start: 0.2084 (mtp) cc_final: 0.1169 (mmt) REVERT: C 74 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8564 (tp) REVERT: C 121 MET cc_start: 0.5605 (ppp) cc_final: 0.4875 (tpt) REVERT: C 216 LYS cc_start: 0.9332 (ptmt) cc_final: 0.9097 (ptpp) REVERT: C 232 TRP cc_start: 0.4856 (t60) cc_final: 0.3535 (t60) REVERT: D 100 MET cc_start: 0.7900 (ppp) cc_final: 0.7510 (ppp) REVERT: E 15 PHE cc_start: 0.3724 (OUTLIER) cc_final: 0.3304 (m-10) REVERT: E 31 MET cc_start: 0.5586 (tpt) cc_final: 0.5176 (ttt) REVERT: H 110 LYS cc_start: 0.8057 (mttt) cc_final: 0.7137 (tptp) REVERT: H 209 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3377 (mt) REVERT: J 55 LEU cc_start: 0.3500 (pt) cc_final: 0.3053 (tp) REVERT: J 77 ASN cc_start: 0.7279 (t0) cc_final: 0.6995 (t0) REVERT: J 90 LEU cc_start: -0.0848 (OUTLIER) cc_final: -0.1190 (mp) outliers start: 86 outliers final: 41 residues processed: 310 average time/residue: 0.2992 time to fit residues: 143.0822 Evaluate side-chains 264 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 220 LEU 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 443 TRP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 552 SER 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 691 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 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 165 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 15 PHE 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 81 ASP Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS 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 90 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 147 THR 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 31 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 722 GLN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 GLN B 26 ASN B 120 ASN B 145 ASN B 159 HIS B 167 ASN B 169 HIS B 296 GLN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN E 86 ASN E 94 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 158 HIS J 141 HIS J 149 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.097861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.081508 restraints weight = 84410.991| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 5.89 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.9780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 18899 Z= 0.335 Angle : 1.132 16.679 25618 Z= 0.578 Chirality : 0.058 0.411 2889 Planarity : 0.008 0.090 3236 Dihedral : 6.546 58.321 2686 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.29 % Favored : 90.36 % Rotamer: Outliers : 6.49 % Allowed : 26.81 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2271 helix: 0.37 (0.17), residues: 837 sheet: -0.43 (0.23), residues: 469 loop : -3.20 (0.16), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 110 HIS 0.019 0.003 HIS A 428 PHE 0.049 0.004 PHE B 230 TYR 0.085 0.004 TYR B 8 ARG 0.037 0.002 ARG A 527 Details of bonding type rmsd link_NAG-ASN : bond 0.01493 ( 3) link_NAG-ASN : angle 4.37892 ( 9) link_BETA1-4 : bond 0.01625 ( 6) link_BETA1-4 : angle 2.27059 ( 18) hydrogen bonds : bond 0.05928 ( 820) hydrogen bonds : angle 6.44591 ( 2397) covalent geometry : bond 0.00717 (18890) covalent geometry : angle 1.12833 (25591) *********************** 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 463 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 333 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 VAL cc_start: 0.6488 (t) cc_final: 0.6182 (t) REVERT: A 336 MET cc_start: 0.7137 (mmm) cc_final: 0.6626 (mmm) REVERT: A 373 TYR cc_start: 0.7488 (m-10) cc_final: 0.6313 (m-80) REVERT: A 443 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.6934 (p-90) REVERT: A 535 MET cc_start: 0.4387 (tpt) cc_final: 0.4099 (ppp) REVERT: A 536 MET cc_start: 0.4837 (ppp) cc_final: 0.4578 (ppp) REVERT: A 546 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3642 (t80) REVERT: A 749 ASP cc_start: 0.7152 (p0) cc_final: 0.6934 (p0) REVERT: A 779 LYS cc_start: 0.4117 (tptt) cc_final: 0.3622 (mmtm) REVERT: A 832 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: A 848 GLU cc_start: 0.8056 (tp30) cc_final: 0.7361 (tp30) REVERT: A 962 TYR cc_start: 0.0725 (OUTLIER) cc_final: -0.0377 (m-80) REVERT: B 55 ILE cc_start: 0.5889 (mm) cc_final: 0.5674 (mm) REVERT: B 117 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6461 (p0) REVERT: C 74 LEU cc_start: 0.9189 (mm) cc_final: 0.8794 (tp) REVERT: C 147 ARG cc_start: 0.4026 (mtt180) cc_final: 0.3104 (mtm180) REVERT: C 232 TRP cc_start: 0.6446 (t60) cc_final: 0.6228 (t60) REVERT: D 100 MET cc_start: 0.8196 (ppp) cc_final: 0.7854 (ppp) REVERT: E 31 MET cc_start: 0.6248 (tpt) cc_final: 0.5969 (ttt) REVERT: F 84 LEU cc_start: 0.5671 (mp) cc_final: 0.5203 (mm) REVERT: F 85 PHE cc_start: 0.1245 (OUTLIER) cc_final: 0.0994 (t80) REVERT: H 94 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: H 110 LYS cc_start: 0.8371 (mttt) cc_final: 0.7747 (pttt) REVERT: H 174 LEU cc_start: 0.8144 (mt) cc_final: 0.7778 (mt) REVERT: H 209 LEU cc_start: 0.3807 (OUTLIER) cc_final: 0.3565 (mm) REVERT: J 55 LEU cc_start: 0.4798 (pt) cc_final: 0.4274 (tp) REVERT: J 77 ASN cc_start: 0.8217 (t0) cc_final: 0.7563 (t0) outliers start: 130 outliers final: 58 residues processed: 435 average time/residue: 0.3219 time to fit residues: 217.7610 Evaluate side-chains 346 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 280 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 588 THR 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 691 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 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 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 25 VAL 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 94 GLN 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 147 THR Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 191 optimal weight: 0.2980 chunk 192 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 771 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 296 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.098934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.082393 restraints weight = 83696.132| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.97 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 1.0183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18899 Z= 0.160 Angle : 0.830 15.292 25618 Z= 0.401 Chirality : 0.046 0.378 2889 Planarity : 0.005 0.061 3236 Dihedral : 5.543 59.267 2686 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.01 % Favored : 91.63 % Rotamer: Outliers : 4.59 % Allowed : 30.55 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2271 helix: 0.88 (0.18), residues: 852 sheet: -0.14 (0.23), residues: 478 loop : -3.05 (0.17), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 17 HIS 0.011 0.001 HIS H 23 PHE 0.064 0.002 PHE B 230 TYR 0.030 0.002 TYR E 30 ARG 0.007 0.001 ARG J 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 3) link_NAG-ASN : angle 3.44806 ( 9) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 1.67479 ( 18) hydrogen bonds : bond 0.04071 ( 820) hydrogen bonds : angle 5.43456 ( 2397) covalent geometry : bond 0.00356 (18890) covalent geometry : angle 0.82722 (25591) *********************** 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 385 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 293 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7467 (mtt) cc_final: 0.7231 (mtt) REVERT: A 336 MET cc_start: 0.7103 (mmm) cc_final: 0.6635 (mmm) REVERT: A 536 MET cc_start: 0.4478 (ppp) cc_final: 0.3686 (ptm) REVERT: A 619 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5890 (mm) REVERT: A 848 GLU cc_start: 0.7695 (tp30) cc_final: 0.7181 (tp30) REVERT: A 919 MET cc_start: 0.8387 (mmm) cc_final: 0.7951 (mmp) REVERT: A 957 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7144 (ttpt) REVERT: B 32 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7416 (pp30) REVERT: B 61 ILE cc_start: 0.7701 (mm) cc_final: 0.7285 (mm) REVERT: B 115 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: C 51 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8696 (p0) REVERT: C 74 LEU cc_start: 0.9177 (mm) cc_final: 0.8758 (tp) REVERT: C 121 MET cc_start: 0.6522 (ttp) cc_final: 0.5785 (tpp) REVERT: C 172 TYR cc_start: 0.3757 (t80) cc_final: 0.3222 (t80) REVERT: C 232 TRP cc_start: 0.6207 (t60) cc_final: 0.5723 (t60) REVERT: D 100 MET cc_start: 0.8381 (ppp) cc_final: 0.8110 (ppp) REVERT: E 31 MET cc_start: 0.6084 (tpt) cc_final: 0.5704 (ttt) REVERT: F 84 LEU cc_start: 0.5321 (mp) cc_final: 0.5111 (mm) REVERT: G 124 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7540 (t0) REVERT: H 110 LYS cc_start: 0.8425 (mttt) cc_final: 0.7801 (pttt) REVERT: H 134 MET cc_start: 0.5247 (pmm) cc_final: 0.4784 (pmm) REVERT: H 174 LEU cc_start: 0.8177 (mt) cc_final: 0.7854 (mt) REVERT: H 203 ASN cc_start: 0.8341 (m-40) cc_final: 0.7915 (m-40) REVERT: H 209 LEU cc_start: 0.3932 (OUTLIER) cc_final: 0.3676 (mm) REVERT: J 55 LEU cc_start: 0.5061 (pt) cc_final: 0.4783 (tp) REVERT: J 77 ASN cc_start: 0.8039 (t0) cc_final: 0.7615 (t0) REVERT: J 174 GLU cc_start: 0.7981 (pm20) cc_final: 0.7589 (pm20) outliers start: 92 outliers final: 59 residues processed: 367 average time/residue: 0.3930 time to fit residues: 229.3970 Evaluate side-chains 321 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 201 LYS 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 366 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 619 LEU 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 691 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 860 HIS 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 957 LYS Chi-restraints excluded: chain A residue 958 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 138 THR 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 D residue 120 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE 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 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 64 THR 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 73 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 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 200 optimal weight: 0.5980 chunk 204 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 212 GLN ** 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 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 194 GLN B 296 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.098747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.082104 restraints weight = 82007.954| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 5.92 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 1.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18899 Z= 0.153 Angle : 0.818 16.073 25618 Z= 0.395 Chirality : 0.045 0.349 2889 Planarity : 0.005 0.061 3236 Dihedral : 5.266 59.378 2686 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.01 % Favored : 91.63 % Rotamer: Outliers : 4.04 % Allowed : 31.75 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2271 helix: 1.12 (0.18), residues: 847 sheet: -0.02 (0.23), residues: 480 loop : -3.00 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 197 HIS 0.023 0.001 HIS H 62 PHE 0.063 0.002 PHE B 230 TYR 0.032 0.002 TYR E 30 ARG 0.012 0.001 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 3) link_NAG-ASN : angle 3.13534 ( 9) link_BETA1-4 : bond 0.00302 ( 6) link_BETA1-4 : angle 1.54902 ( 18) hydrogen bonds : bond 0.03858 ( 820) hydrogen bonds : angle 5.21917 ( 2397) covalent geometry : bond 0.00341 (18890) covalent geometry : angle 0.81528 (25591) *********************** 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 348 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 267 time to evaluate : 2.319 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 35 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.5862 (tt0) REVERT: A 107 MET cc_start: 0.6392 (ppp) cc_final: 0.6018 (tmm) REVERT: A 177 MET cc_start: 0.7304 (mtt) cc_final: 0.7028 (mtt) REVERT: A 536 MET cc_start: 0.4555 (ppp) cc_final: 0.3958 (ptm) REVERT: A 619 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5933 (mm) REVERT: B 32 GLN cc_start: 0.8028 (pp30) cc_final: 0.7485 (pp30) REVERT: C 51 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8693 (p0) REVERT: C 74 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 121 MET cc_start: 0.6654 (ttp) cc_final: 0.6041 (tpp) REVERT: C 147 ARG cc_start: 0.4047 (mpt180) cc_final: 0.3683 (mtm110) REVERT: C 232 TRP cc_start: 0.6279 (t60) cc_final: 0.5834 (t60) REVERT: D 100 MET cc_start: 0.8429 (ppp) cc_final: 0.8181 (ppp) REVERT: E 31 MET cc_start: 0.6183 (tpt) cc_final: 0.5698 (ttt) REVERT: F 84 LEU cc_start: 0.5621 (mp) cc_final: 0.5339 (mm) REVERT: H 110 LYS cc_start: 0.8422 (mttt) cc_final: 0.7665 (tptp) REVERT: H 174 LEU cc_start: 0.8402 (mt) cc_final: 0.8025 (mt) REVERT: J 55 LEU cc_start: 0.5155 (pt) cc_final: 0.4868 (tp) REVERT: J 77 ASN cc_start: 0.8119 (t0) cc_final: 0.7693 (t0) outliers start: 81 outliers final: 52 residues processed: 334 average time/residue: 0.4132 time to fit residues: 218.9954 Evaluate side-chains 311 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 422 LEU 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 538 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 632 MET 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 691 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 860 HIS 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 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 64 THR 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 147 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 182 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** 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 722 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN E 19 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN H 147 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.096610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.079395 restraints weight = 84097.929| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 6.05 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 1.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18899 Z= 0.187 Angle : 0.876 17.900 25618 Z= 0.429 Chirality : 0.047 0.385 2889 Planarity : 0.006 0.106 3236 Dihedral : 5.208 58.816 2684 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.45 % Favored : 91.19 % Rotamer: Outliers : 4.14 % Allowed : 31.80 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2271 helix: 1.11 (0.18), residues: 840 sheet: -0.11 (0.23), residues: 483 loop : -3.05 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 32 HIS 0.015 0.002 HIS A 428 PHE 0.055 0.002 PHE B 230 TYR 0.041 0.002 TYR B 8 ARG 0.015 0.001 ARG A 660 Details of bonding type rmsd link_NAG-ASN : bond 0.00881 ( 3) link_NAG-ASN : angle 3.43933 ( 9) link_BETA1-4 : bond 0.00496 ( 6) link_BETA1-4 : angle 1.68650 ( 18) hydrogen bonds : bond 0.04391 ( 820) hydrogen bonds : angle 5.27799 ( 2397) covalent geometry : bond 0.00408 (18890) covalent geometry : angle 0.87319 (25591) *********************** 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 383 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6146 (mttp) REVERT: A 177 MET cc_start: 0.7159 (mtt) cc_final: 0.6881 (mtt) REVERT: A 336 MET cc_start: 0.7211 (mmm) cc_final: 0.7010 (mmm) REVERT: A 457 MET cc_start: 0.6196 (mmt) cc_final: 0.5787 (mmt) REVERT: A 535 MET cc_start: 0.5494 (tpt) cc_final: 0.5153 (ttm) REVERT: A 619 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6696 (mm) REVERT: A 794 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: A 863 ILE cc_start: 0.8446 (tp) cc_final: 0.8163 (tp) REVERT: A 898 TYR cc_start: 0.5546 (t80) cc_final: 0.5046 (t80) REVERT: B 32 GLN cc_start: 0.7994 (pp30) cc_final: 0.7600 (pp30) REVERT: B 117 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6436 (p0) REVERT: C 51 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8676 (p0) REVERT: C 74 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8843 (tp) REVERT: C 121 MET cc_start: 0.6983 (ttp) cc_final: 0.6155 (tpp) REVERT: C 185 LEU cc_start: 0.7256 (tt) cc_final: 0.6958 (tt) REVERT: C 232 TRP cc_start: 0.6642 (t60) cc_final: 0.6267 (t60) REVERT: D 100 MET cc_start: 0.8519 (ppp) cc_final: 0.8235 (ppp) REVERT: E 31 MET cc_start: 0.6410 (tpt) cc_final: 0.5714 (ttt) REVERT: H 61 PHE cc_start: 0.8065 (t80) cc_final: 0.7786 (t80) REVERT: H 72 GLU cc_start: 0.6691 (tp30) cc_final: 0.6327 (mm-30) REVERT: H 110 LYS cc_start: 0.8538 (mttt) cc_final: 0.7702 (tptp) REVERT: H 170 ILE cc_start: 0.6540 (tt) cc_final: 0.6050 (tt) REVERT: H 174 LEU cc_start: 0.8652 (mt) cc_final: 0.8246 (mt) REVERT: H 175 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6787 (pp) REVERT: J 55 LEU cc_start: 0.5647 (pt) cc_final: 0.5399 (tp) REVERT: J 77 ASN cc_start: 0.8360 (t0) cc_final: 0.8045 (t0) outliers start: 83 outliers final: 54 residues processed: 357 average time/residue: 0.2888 time to fit residues: 163.2350 Evaluate side-chains 327 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 632 MET 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 710 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU 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 85 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 HIS 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 97 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU 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 84 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 40 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** 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 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS ** 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 = 0.4143 r_free = 0.4143 target = 0.097457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.080018 restraints weight = 83599.374| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 6.22 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 1.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18899 Z= 0.147 Angle : 0.844 16.587 25618 Z= 0.401 Chirality : 0.045 0.349 2889 Planarity : 0.005 0.059 3236 Dihedral : 5.018 59.902 2684 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.88 % Favored : 91.77 % Rotamer: Outliers : 3.00 % Allowed : 34.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2271 helix: 1.15 (0.18), residues: 847 sheet: 0.07 (0.23), residues: 484 loop : -3.02 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.014 0.001 HIS A 428 PHE 0.062 0.002 PHE B 230 TYR 0.036 0.001 TYR E 30 ARG 0.015 0.001 ARG A 660 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 3) link_NAG-ASN : angle 3.01103 ( 9) link_BETA1-4 : bond 0.00294 ( 6) link_BETA1-4 : angle 1.57784 ( 18) hydrogen bonds : bond 0.03721 ( 820) hydrogen bonds : angle 5.09329 ( 2397) covalent geometry : bond 0.00323 (18890) covalent geometry : angle 0.84140 (25591) *********************** 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 352 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7229 (mtt) cc_final: 0.6960 (mtt) REVERT: A 535 MET cc_start: 0.5693 (tpt) cc_final: 0.5198 (ttm) REVERT: A 619 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6618 (mm) REVERT: A 848 GLU cc_start: 0.7777 (tp30) cc_final: 0.7205 (tp30) REVERT: B 32 GLN cc_start: 0.8112 (pp30) cc_final: 0.7468 (pp30) REVERT: B 115 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: C 6 LEU cc_start: 0.7779 (tp) cc_final: 0.7494 (tp) REVERT: C 51 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8713 (p0) REVERT: C 74 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8843 (tp) REVERT: C 121 MET cc_start: 0.6951 (ttp) cc_final: 0.6329 (tpp) REVERT: C 151 MET cc_start: 0.8113 (mmp) cc_final: 0.7771 (mtt) REVERT: C 232 TRP cc_start: 0.6535 (t60) cc_final: 0.6095 (t60) REVERT: D 100 MET cc_start: 0.8497 (ppp) cc_final: 0.8245 (ppp) REVERT: D 104 MET cc_start: 0.7028 (tpp) cc_final: 0.6797 (tmm) REVERT: D 172 GLU cc_start: 0.7450 (tp30) cc_final: 0.6730 (tm-30) REVERT: H 64 THR cc_start: 0.7060 (m) cc_final: 0.6854 (m) REVERT: H 110 LYS cc_start: 0.8582 (mttt) cc_final: 0.7695 (tptp) REVERT: H 174 LEU cc_start: 0.8646 (mt) cc_final: 0.8276 (mt) REVERT: H 175 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6768 (pp) REVERT: J 77 ASN cc_start: 0.8282 (t0) cc_final: 0.7863 (t0) REVERT: J 80 ASP cc_start: 0.6120 (m-30) cc_final: 0.5781 (m-30) outliers start: 60 outliers final: 48 residues processed: 337 average time/residue: 0.2713 time to fit residues: 144.9634 Evaluate side-chains 321 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 632 MET 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 741 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 30 ILE 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 222 TRP Chi-restraints excluded: chain D residue 96 ILE 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 E residue 95 HIS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 27 ASP 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 G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU 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 147 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 218 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 213 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** 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 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 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 = 0.4141 r_free = 0.4141 target = 0.097298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.079950 restraints weight = 84060.491| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 6.12 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 1.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18899 Z= 0.145 Angle : 0.852 15.990 25618 Z= 0.403 Chirality : 0.045 0.348 2889 Planarity : 0.005 0.059 3236 Dihedral : 4.922 59.535 2684 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.10 % Favored : 91.55 % Rotamer: Outliers : 2.75 % Allowed : 34.70 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2271 helix: 1.13 (0.18), residues: 847 sheet: 0.30 (0.24), residues: 479 loop : -2.98 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 110 HIS 0.014 0.001 HIS A 428 PHE 0.062 0.002 PHE B 230 TYR 0.047 0.001 TYR B 8 ARG 0.010 0.001 ARG A 660 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 3) link_NAG-ASN : angle 2.93550 ( 9) link_BETA1-4 : bond 0.00321 ( 6) link_BETA1-4 : angle 1.57532 ( 18) hydrogen bonds : bond 0.03739 ( 820) hydrogen bonds : angle 5.04997 ( 2397) covalent geometry : bond 0.00322 (18890) covalent geometry : angle 0.84961 (25591) ********************** 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 337 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 2.369 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: 0.6940 (tp40) cc_final: 0.6643 (tt0) REVERT: A 177 MET cc_start: 0.7220 (mtt) cc_final: 0.6957 (mtt) REVERT: A 366 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (pp) REVERT: A 535 MET cc_start: 0.5918 (tpt) cc_final: 0.5100 (ttm) REVERT: A 619 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6549 (mm) REVERT: A 848 GLU cc_start: 0.7719 (tp30) cc_final: 0.7397 (tm-30) REVERT: A 856 ILE cc_start: 0.5737 (tp) cc_final: 0.5163 (mm) REVERT: B 32 GLN cc_start: 0.8065 (pp30) cc_final: 0.7571 (pp30) REVERT: B 75 CYS cc_start: 0.7490 (m) cc_final: 0.6796 (t) REVERT: B 183 MET cc_start: 0.6884 (ttp) cc_final: 0.6532 (ptt) REVERT: C 51 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8660 (p0) REVERT: C 74 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8829 (tp) REVERT: C 121 MET cc_start: 0.6993 (ttp) cc_final: 0.6391 (tpp) REVERT: C 151 MET cc_start: 0.8039 (mmp) cc_final: 0.7752 (mtt) REVERT: C 162 ASP cc_start: 0.8235 (p0) cc_final: 0.8028 (p0) REVERT: C 232 TRP cc_start: 0.6468 (t60) cc_final: 0.6101 (t60) REVERT: D 154 MET cc_start: 0.6173 (tpp) cc_final: 0.4489 (mtm) REVERT: D 172 GLU cc_start: 0.7491 (tp30) cc_final: 0.6851 (tm-30) REVERT: H 61 PHE cc_start: 0.8159 (t80) cc_final: 0.7888 (t80) REVERT: H 64 THR cc_start: 0.7314 (m) cc_final: 0.7099 (m) REVERT: H 110 LYS cc_start: 0.8529 (mttt) cc_final: 0.7681 (tptp) REVERT: H 174 LEU cc_start: 0.8642 (mt) cc_final: 0.8265 (mt) REVERT: H 175 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6898 (pp) REVERT: J 77 ASN cc_start: 0.8318 (t0) cc_final: 0.8010 (t0) outliers start: 55 outliers final: 46 residues processed: 324 average time/residue: 0.2516 time to fit residues: 132.7160 Evaluate side-chains 320 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 632 MET 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 782 VAL Chi-restraints excluded: chain A residue 834 LEU 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 152 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 30 ILE 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 138 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 27 ASP 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 G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 65 LEU 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 147 THR Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 19 optimal weight: 10.0000 chunk 155 optimal weight: 0.0070 chunk 6 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 169 optimal weight: 0.0470 chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 0.0570 chunk 148 optimal weight: 7.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** 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 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.098200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.080890 restraints weight = 82292.641| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 6.06 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 1.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18899 Z= 0.140 Angle : 0.842 15.786 25618 Z= 0.398 Chirality : 0.045 0.333 2889 Planarity : 0.005 0.060 3236 Dihedral : 4.825 59.554 2684 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.75 % Favored : 91.90 % Rotamer: Outliers : 2.70 % Allowed : 34.95 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2271 helix: 1.14 (0.18), residues: 847 sheet: 0.40 (0.24), residues: 475 loop : -2.96 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 15 HIS 0.014 0.001 HIS A 428 PHE 0.059 0.001 PHE B 230 TYR 0.029 0.001 TYR E 30 ARG 0.009 0.001 ARG A 660 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 3) link_NAG-ASN : angle 2.74559 ( 9) link_BETA1-4 : bond 0.00287 ( 6) link_BETA1-4 : angle 1.50651 ( 18) hydrogen bonds : bond 0.03620 ( 820) hydrogen bonds : angle 5.01190 ( 2397) covalent geometry : bond 0.00309 (18890) covalent geometry : angle 0.84003 (25591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9196.05 seconds wall clock time: 164 minutes 2.72 seconds (9842.72 seconds total)