Starting phenix.real_space_refine on Fri Sep 11 21:21:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.cif Found real_map, /net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6idf_9648/09_2026/6idf_9648.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 7344 2.51 5 N 1762 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11188 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 263 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 2.40, per 1000 atoms: 0.21 Number of scatterers: 11188 At special positions: 0 Unit cell: (110.191, 94.917, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 4 15.00 O 2034 8.00 N 1762 7.00 C 7344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS E 9 " distance=2.03 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=1, symmetry=0 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 810 " - " ASN A 387 " " NAG A 817 " - " ASN A 464 " " NAG A 818 " - " ASN A 506 " " NAG A 819 " - " ASN A 264 " " NAG A 820 " - " ASN A 187 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 502.1 milliseconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 57.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.563A pdb=" N ILE A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.137A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.170A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.934A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.524A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.737A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.998A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.901A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.572A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 405 removed outlier: 3.561A pdb=" N ASP A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.712A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.677A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.743A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.560A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 74 through 103 removed outlier: 3.902A pdb=" N HIS B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 154 removed outlier: 3.881A pdb=" N HIS B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.920A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 4.334A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.609A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 removed outlier: 3.764A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 240 removed outlier: 4.081A pdb=" N GLN B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.552A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.864A pdb=" N MET B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.871A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.511A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.306A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.564A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 28 through 60 removed outlier: 4.256A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 107 removed outlier: 3.712A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.785A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.929A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.819A pdb=" N ASN C 207 " --> pdb=" O THR C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.756A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'D' and resid 7 through 21 removed outlier: 4.058A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 42 removed outlier: 3.845A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.570A pdb=" N TYR D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 4.050A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.675A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.661A pdb=" N THR E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 8' Processing helix chain 'E' and resid 16 through 23 removed outlier: 4.278A pdb=" N VAL E 20 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.497A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 222 removed outlier: 4.029A pdb=" N ARG A 652 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 8.976A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.299A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.661A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.517A pdb=" N LEU E 36 " --> pdb=" O GLY B 382 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1572 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: 1.79 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.44: 3232 1.44 - 1.57: 6471 1.57 - 1.70: 13 1.70 - 1.83: 66 Bond restraints: 11462 Sorted by residual: bond pdb=" C29 PC1 C 301 " pdb=" C2A PC1 C 301 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C29 PC1 B 501 " pdb=" C2A PC1 B 501 " ideal model delta sigma weight residual 1.524 1.348 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C29 PC1 B 502 " pdb=" C2A PC1 B 502 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C29 PC1 D 201 " pdb=" C2A PC1 D 201 " ideal model delta sigma weight residual 1.524 1.349 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C31 PC1 B 502 " pdb=" O31 PC1 B 502 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 15463 4.70 - 9.39: 143 9.39 - 14.09: 5 14.09 - 18.78: 0 18.78 - 23.48: 4 Bond angle restraints: 15615 Sorted by residual: angle pdb=" O12 PC1 C 301 " pdb=" P PC1 C 301 " pdb=" O14 PC1 C 301 " ideal model delta sigma weight residual 123.67 100.19 23.48 3.00e+00 1.11e-01 6.12e+01 angle pdb=" O12 PC1 B 501 " pdb=" P PC1 B 501 " pdb=" O14 PC1 B 501 " ideal model delta sigma weight residual 123.67 101.07 22.60 3.00e+00 1.11e-01 5.68e+01 angle pdb=" O12 PC1 D 201 " pdb=" P PC1 D 201 " pdb=" O14 PC1 D 201 " ideal model delta sigma weight residual 123.67 101.14 22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 101.17 22.50 3.00e+00 1.11e-01 5.62e+01 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.44e+01 ... (remaining 15610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 6126 16.79 - 33.59: 287 33.59 - 50.38: 89 50.38 - 67.18: 15 67.18 - 83.97: 11 Dihedral angle restraints: 6528 sinusoidal: 2551 harmonic: 3977 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -169.97 83.97 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.97 78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 ... (remaining 6525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1707 0.097 - 0.194: 146 0.194 - 0.291: 10 0.291 - 0.388: 3 0.388 - 0.485: 2 Chirality restraints: 1868 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.01 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG A 819 " pdb=" ND2 ASN A 264 " pdb=" C2 NAG A 819 " pdb=" O5 NAG A 819 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1865 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 211 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.020 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP C 227 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 560 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.036 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2836 2.80 - 3.33: 9763 3.33 - 3.85: 17960 3.85 - 4.38: 20803 4.38 - 4.90: 36230 Nonbonded interactions: 87592 Sorted by model distance: nonbonded pdb=" O VAL A 383 " pdb=" O6 NAG H 1 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.285 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.318 3.040 nonbonded pdb=" O PHE C 162 " pdb=" OH TYR C 218 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.329 3.040 ... (remaining 87587 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 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.008 0.177 11488 Z= 0.380 Angle : 1.201 23.476 15685 Z= 0.563 Chirality : 0.059 0.485 1868 Planarity : 0.007 0.084 1877 Dihedral : 11.840 75.882 3947 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 0.44 % Allowed : 2.99 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.17), residues: 1351 helix: -2.36 (0.14), residues: 697 sheet: -1.88 (0.43), residues: 125 loop : -3.14 (0.21), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 432 TYR 0.030 0.002 TYR A 565 PHE 0.041 0.003 PHE C 132 TRP 0.045 0.004 TRP C 227 HIS 0.012 0.003 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.38 (11462) covalent geometry : angle 1.17263 / 0.56 (15615) SS BOND : bond 0.00505 / 0.26 ( 5) SS BOND : angle 2.42310 / 1.39 ( 10) hydrogen bonds : bond 0.15547 / 11.00 ( 545) hydrogen bonds : angle 6.64183 / 4.61 ( 1572) Misc. bond : bond 0.00363 / 0.19 ( 1) link_BETA1-3 : bond 0.00608 / 0.32 ( 1) link_BETA1-3 : angle 1.96120 / 1.08 ( 3) link_BETA1-4 : bond 0.01683 / 1.09 ( 7) link_BETA1-4 : angle 3.56597 / 2.38 ( 21) link_BETA1-6 : bond 0.00663 / 0.35 ( 1) link_BETA1-6 : angle 1.33488 / 1.01 ( 3) link_NAG-ASN : bond 0.01034 / 0.54 ( 11) link_NAG-ASN : angle 4.91600 / 3.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 PHE cc_start: 0.8577 (m-80) cc_final: 0.8260 (m-80) REVERT: B 165 TRP cc_start: 0.7314 (t60) cc_final: 0.6977 (t60) REVERT: B 248 LEU cc_start: 0.8061 (mt) cc_final: 0.7522 (tm) REVERT: B 259 VAL cc_start: 0.7387 (p) cc_final: 0.7093 (m) REVERT: C 117 MET cc_start: 0.8093 (mtm) cc_final: 0.7874 (mtt) outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 0.5650 time to fit residues: 136.0300 Evaluate side-chains 128 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 158 HIS A 305 GLN A 331 GLN A 358 ASN A 454 GLN A 531 ASN A 587 GLN A 606 GLN B 81 HIS D 50 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112395 restraints weight = 14399.923| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.28 r_work: 0.3156 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11488 Z= 0.168 Angle : 0.727 10.557 15685 Z= 0.351 Chirality : 0.046 0.379 1868 Planarity : 0.006 0.099 1877 Dihedral : 9.747 58.682 1622 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.95 % Allowed : 9.66 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1351 helix: -0.45 (0.19), residues: 705 sheet: -1.61 (0.42), residues: 131 loop : -2.91 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 432 TYR 0.016 0.002 TYR D 91 PHE 0.040 0.002 PHE A 302 TRP 0.023 0.002 TRP C 227 HIS 0.008 0.002 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (11462) covalent geometry : angle 0.70284 / 0.35 (15615) SS BOND : bond 0.00623 / 0.31 ( 5) SS BOND : angle 2.11470 / 1.55 ( 10) hydrogen bonds : bond 0.04710 / 3.17 ( 545) hydrogen bonds : angle 4.66657 / 3.30 ( 1572) Misc. bond : bond 0.00189 / 0.10 ( 1) link_BETA1-3 : bond 0.00379 / 0.20 ( 1) link_BETA1-3 : angle 1.73937 / 1.18 ( 3) link_BETA1-4 : bond 0.00576 / 0.36 ( 7) link_BETA1-4 : angle 2.06327 / 1.42 ( 21) link_BETA1-6 : bond 0.01210 / 0.64 ( 1) link_BETA1-6 : angle 1.49893 / 1.05 ( 3) link_NAG-ASN : bond 0.00625 / 0.33 ( 11) link_NAG-ASN : angle 3.62229 / 2.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8839 (mptm) cc_final: 0.8513 (mppt) REVERT: A 55 ASN cc_start: 0.8235 (t0) cc_final: 0.7968 (t0) REVERT: A 78 LYS cc_start: 0.8273 (ptpt) cc_final: 0.7955 (pttt) REVERT: A 80 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7617 (tp30) REVERT: A 231 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8531 (mmm) REVERT: A 474 GLU cc_start: 0.8186 (tp30) cc_final: 0.7976 (tp30) REVERT: A 583 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6824 (ttt180) REVERT: A 601 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: A 657 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8640 (ptt-90) REVERT: B 165 TRP cc_start: 0.7294 (t60) cc_final: 0.7081 (t60) REVERT: B 248 LEU cc_start: 0.7700 (mt) cc_final: 0.7301 (tm) REVERT: B 259 VAL cc_start: 0.7274 (p) cc_final: 0.6895 (m) REVERT: C 240 GLN cc_start: 0.7774 (mt0) cc_final: 0.7444 (mt0) outliers start: 45 outliers final: 16 residues processed: 159 average time/residue: 0.5937 time to fit residues: 101.8890 Evaluate side-chains 133 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 194 GLN A 553 HIS A 587 GLN B 135 ASN B 222 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107449 restraints weight = 14346.270| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.14 r_work: 0.3056 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11488 Z= 0.230 Angle : 0.765 12.317 15685 Z= 0.370 Chirality : 0.048 0.383 1868 Planarity : 0.005 0.096 1877 Dihedral : 9.497 58.722 1622 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.30 % Allowed : 11.94 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.22), residues: 1351 helix: 0.04 (0.19), residues: 717 sheet: -1.48 (0.41), residues: 134 loop : -2.68 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.020 0.002 TYR B 225 PHE 0.040 0.002 PHE A 302 TRP 0.016 0.002 TRP C 209 HIS 0.010 0.002 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (11462) covalent geometry : angle 0.74472 / 0.37 (15615) SS BOND : bond 0.00494 / 0.25 ( 5) SS BOND : angle 1.83632 / 1.14 ( 10) hydrogen bonds : bond 0.05158 / 3.47 ( 545) hydrogen bonds : angle 4.47616 / 3.13 ( 1572) Misc. bond : bond 0.00226 / 0.12 ( 1) link_BETA1-3 : bond 0.00228 / 0.12 ( 1) link_BETA1-3 : angle 1.42791 / 0.85 ( 3) link_BETA1-4 : bond 0.00738 / 0.48 ( 7) link_BETA1-4 : angle 2.21136 / 1.50 ( 21) link_BETA1-6 : bond 0.01185 / 0.62 ( 1) link_BETA1-6 : angle 1.80533 / 1.44 ( 3) link_NAG-ASN : bond 0.00649 / 0.32 ( 11) link_NAG-ASN : angle 3.36800 / 2.57 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8859 (mptm) cc_final: 0.8485 (mppt) REVERT: A 78 LYS cc_start: 0.8319 (ptpt) cc_final: 0.8077 (pttt) REVERT: A 80 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7651 (tp30) REVERT: A 474 GLU cc_start: 0.8140 (tp30) cc_final: 0.7893 (tp30) REVERT: A 583 ARG cc_start: 0.7520 (ttp80) cc_final: 0.6985 (ttt180) REVERT: A 601 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 657 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8655 (ptt-90) REVERT: A 669 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: B 248 LEU cc_start: 0.7721 (mt) cc_final: 0.7333 (tm) REVERT: B 259 VAL cc_start: 0.7303 (p) cc_final: 0.6956 (m) REVERT: C 211 GLU cc_start: 0.8627 (pt0) cc_final: 0.8409 (pm20) REVERT: D 26 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8885 (mt) REVERT: D 54 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7366 (ttpt) outliers start: 49 outliers final: 24 residues processed: 150 average time/residue: 0.5840 time to fit residues: 94.5477 Evaluate side-chains 140 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 124 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 142 ASN A 587 GLN B 222 GLN C 240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102809 restraints weight = 14303.312| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.21 r_work: 0.3010 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11488 Z= 0.250 Angle : 0.778 13.661 15685 Z= 0.376 Chirality : 0.049 0.386 1868 Planarity : 0.005 0.092 1877 Dihedral : 9.342 59.679 1622 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.48 % Allowed : 12.82 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1351 helix: 0.26 (0.20), residues: 722 sheet: -1.34 (0.40), residues: 134 loop : -2.50 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 237 TYR 0.024 0.002 TYR D 18 PHE 0.042 0.002 PHE A 302 TRP 0.014 0.002 TRP B 165 HIS 0.012 0.002 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (11462) covalent geometry : angle 0.75922 / 0.37 (15615) SS BOND : bond 0.00526 / 0.27 ( 5) SS BOND : angle 1.68179 / 0.94 ( 10) hydrogen bonds : bond 0.05234 / 3.52 ( 545) hydrogen bonds : angle 4.39450 / 3.08 ( 1572) Misc. bond : bond 0.00217 / 0.11 ( 1) link_BETA1-3 : bond 0.00348 / 0.18 ( 1) link_BETA1-3 : angle 1.15957 / 0.68 ( 3) link_BETA1-4 : bond 0.00682 / 0.44 ( 7) link_BETA1-4 : angle 2.27364 / 1.51 ( 21) link_BETA1-6 : bond 0.00924 / 0.49 ( 1) link_BETA1-6 : angle 1.73709 / 1.41 ( 3) link_NAG-ASN : bond 0.00645 / 0.31 ( 11) link_NAG-ASN : angle 3.22228 / 2.51 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8832 (mptm) cc_final: 0.8421 (mppt) REVERT: A 80 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7649 (tp30) REVERT: A 237 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 364 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: A 408 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 474 GLU cc_start: 0.8179 (tp30) cc_final: 0.7906 (tp30) REVERT: A 583 ARG cc_start: 0.7510 (ttp80) cc_final: 0.6978 (ttt180) REVERT: A 598 ASP cc_start: 0.7890 (t0) cc_final: 0.7506 (m-30) REVERT: A 601 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: A 657 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8614 (ptt-90) REVERT: A 667 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7339 (tt0) REVERT: A 669 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: B 248 LEU cc_start: 0.7631 (mt) cc_final: 0.7249 (tm) REVERT: B 259 VAL cc_start: 0.7292 (p) cc_final: 0.6914 (m) REVERT: C 180 ASP cc_start: 0.8682 (t70) cc_final: 0.8354 (t0) REVERT: C 211 GLU cc_start: 0.8621 (pt0) cc_final: 0.8392 (pm20) outliers start: 51 outliers final: 27 residues processed: 151 average time/residue: 0.5933 time to fit residues: 96.8049 Evaluate side-chains 144 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.0060 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 385 GLN A 587 GLN C 240 GLN D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107430 restraints weight = 14211.644| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.28 r_work: 0.3074 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11488 Z= 0.112 Angle : 0.629 13.194 15685 Z= 0.302 Chirality : 0.043 0.392 1868 Planarity : 0.004 0.080 1877 Dihedral : 8.736 59.771 1622 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.81 % Allowed : 15.63 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1351 helix: 0.78 (0.20), residues: 718 sheet: -0.97 (0.42), residues: 129 loop : -2.30 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.015 0.001 TYR A 569 PHE 0.032 0.001 PHE A 302 TRP 0.023 0.001 TRP B 165 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11462) covalent geometry : angle 0.61545 / 0.30 (15615) SS BOND : bond 0.00298 / 0.17 ( 5) SS BOND : angle 1.03801 / 0.62 ( 10) hydrogen bonds : bond 0.03834 / 2.59 ( 545) hydrogen bonds : angle 4.15575 / 2.92 ( 1572) Misc. bond : bond 0.00152 / 0.08 ( 1) link_BETA1-3 : bond 0.00445 / 0.23 ( 1) link_BETA1-3 : angle 1.01589 / 0.73 ( 3) link_BETA1-4 : bond 0.00787 / 0.51 ( 7) link_BETA1-4 : angle 1.90122 / 1.27 ( 21) link_BETA1-6 : bond 0.00948 / 0.50 ( 1) link_BETA1-6 : angle 1.42381 / 1.05 ( 3) link_NAG-ASN : bond 0.00530 / 0.27 ( 11) link_NAG-ASN : angle 2.38447 / 1.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8657 (mptm) cc_final: 0.8263 (mppt) REVERT: A 75 VAL cc_start: 0.9197 (m) cc_final: 0.8858 (t) REVERT: A 78 LYS cc_start: 0.8238 (ptpt) cc_final: 0.7864 (pttp) REVERT: A 80 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7572 (tp30) REVERT: A 114 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7537 (mtp180) REVERT: A 186 GLU cc_start: 0.7264 (tp30) cc_final: 0.6764 (tm-30) REVERT: A 231 MET cc_start: 0.8921 (tpt) cc_final: 0.8562 (mmm) REVERT: A 237 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: A 408 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7885 (p) REVERT: A 474 GLU cc_start: 0.8097 (tp30) cc_final: 0.7864 (tp30) REVERT: A 583 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7021 (ttt90) REVERT: A 598 ASP cc_start: 0.7871 (t0) cc_final: 0.7551 (m-30) REVERT: A 601 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: A 657 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8581 (ptt-90) REVERT: A 669 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: B 165 TRP cc_start: 0.7306 (t60) cc_final: 0.6999 (t60) REVERT: B 248 LEU cc_start: 0.7608 (mt) cc_final: 0.7252 (tm) REVERT: B 259 VAL cc_start: 0.7173 (p) cc_final: 0.6802 (m) REVERT: C 211 GLU cc_start: 0.8613 (pt0) cc_final: 0.8381 (pm20) REVERT: D 54 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7330 (ttpt) REVERT: D 84 ARG cc_start: 0.8442 (mtt-85) cc_final: 0.7896 (mtp180) outliers start: 32 outliers final: 15 residues processed: 141 average time/residue: 0.6197 time to fit residues: 94.3694 Evaluate side-chains 134 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 5 optimal weight: 0.0020 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 587 GLN C 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106324 restraints weight = 14308.658| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.13 r_work: 0.3056 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11488 Z= 0.139 Angle : 0.648 13.160 15685 Z= 0.310 Chirality : 0.044 0.388 1868 Planarity : 0.004 0.081 1877 Dihedral : 8.606 58.508 1622 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.25 % Allowed : 16.07 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1351 helix: 0.90 (0.20), residues: 720 sheet: -1.02 (0.41), residues: 135 loop : -2.17 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.014 0.001 TYR D 19 PHE 0.033 0.001 PHE A 302 TRP 0.016 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11462) covalent geometry : angle 0.63408 / 0.31 (15615) SS BOND : bond 0.00318 / 0.17 ( 5) SS BOND : angle 1.11610 / 0.61 ( 10) hydrogen bonds : bond 0.03992 / 2.70 ( 545) hydrogen bonds : angle 4.10356 / 2.88 ( 1572) Misc. bond : bond 0.00162 / 0.09 ( 1) link_BETA1-3 : bond 0.00398 / 0.21 ( 1) link_BETA1-3 : angle 1.06231 / 0.70 ( 3) link_BETA1-4 : bond 0.00663 / 0.43 ( 7) link_BETA1-4 : angle 1.89308 / 1.24 ( 21) link_BETA1-6 : bond 0.00832 / 0.44 ( 1) link_BETA1-6 : angle 1.50211 / 1.14 ( 3) link_NAG-ASN : bond 0.00495 / 0.24 ( 11) link_NAG-ASN : angle 2.50115 / 1.88 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8732 (mptm) cc_final: 0.8359 (mppt) REVERT: A 75 VAL cc_start: 0.9246 (m) cc_final: 0.8897 (t) REVERT: A 80 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7688 (tp30) REVERT: A 186 GLU cc_start: 0.7195 (tp30) cc_final: 0.6700 (tm-30) REVERT: A 231 MET cc_start: 0.8904 (tpt) cc_final: 0.8488 (mmm) REVERT: A 237 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: A 364 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 583 ARG cc_start: 0.7550 (ttp80) cc_final: 0.7033 (ttt90) REVERT: A 598 ASP cc_start: 0.7875 (t0) cc_final: 0.7585 (m-30) REVERT: A 601 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 657 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8613 (ptt-90) REVERT: B 165 TRP cc_start: 0.7328 (t60) cc_final: 0.7082 (t60) REVERT: B 248 LEU cc_start: 0.7635 (mt) cc_final: 0.7289 (tm) REVERT: B 259 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6799 (m) outliers start: 37 outliers final: 19 residues processed: 141 average time/residue: 0.6306 time to fit residues: 95.8145 Evaluate side-chains 133 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 169 ASN A 587 GLN C 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106433 restraints weight = 14208.705| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.16 r_work: 0.3046 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11488 Z= 0.133 Angle : 0.636 13.304 15685 Z= 0.306 Chirality : 0.043 0.390 1868 Planarity : 0.004 0.076 1877 Dihedral : 8.470 57.020 1622 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.69 % Allowed : 16.15 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1351 helix: 1.05 (0.20), residues: 718 sheet: -0.96 (0.42), residues: 136 loop : -2.10 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 237 TYR 0.017 0.001 TYR D 19 PHE 0.033 0.001 PHE A 302 TRP 0.015 0.001 TRP B 165 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11462) covalent geometry : angle 0.62233 / 0.30 (15615) SS BOND : bond 0.00286 / 0.15 ( 5) SS BOND : angle 1.04642 / 0.57 ( 10) hydrogen bonds : bond 0.03892 / 2.63 ( 545) hydrogen bonds : angle 4.06622 / 2.85 ( 1572) Misc. bond : bond 0.00163 / 0.09 ( 1) link_BETA1-3 : bond 0.00398 / 0.21 ( 1) link_BETA1-3 : angle 1.03328 / 0.70 ( 3) link_BETA1-4 : bond 0.00635 / 0.41 ( 7) link_BETA1-4 : angle 1.87578 / 1.23 ( 21) link_BETA1-6 : bond 0.00829 / 0.44 ( 1) link_BETA1-6 : angle 1.51856 / 1.15 ( 3) link_NAG-ASN : bond 0.00460 / 0.23 ( 11) link_NAG-ASN : angle 2.45600 / 1.83 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8707 (mptm) cc_final: 0.8326 (mppt) REVERT: A 75 VAL cc_start: 0.9235 (m) cc_final: 0.8886 (t) REVERT: A 80 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7674 (tp30) REVERT: A 186 GLU cc_start: 0.7119 (tp30) cc_final: 0.6623 (tm-30) REVERT: A 231 MET cc_start: 0.8871 (tpt) cc_final: 0.8458 (mmm) REVERT: A 364 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: A 583 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7015 (ttt90) REVERT: A 598 ASP cc_start: 0.7880 (t0) cc_final: 0.7584 (m-30) REVERT: A 601 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 626 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8185 (ptp90) REVERT: A 657 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8576 (ptt-90) REVERT: B 165 TRP cc_start: 0.7320 (t60) cc_final: 0.7048 (t60) REVERT: B 248 LEU cc_start: 0.7592 (mt) cc_final: 0.7256 (tm) REVERT: B 259 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6724 (m) REVERT: C 237 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6744 (mmm160) outliers start: 42 outliers final: 20 residues processed: 149 average time/residue: 0.6008 time to fit residues: 96.7494 Evaluate side-chains 139 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105210 restraints weight = 14138.595| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.21 r_work: 0.3035 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11488 Z= 0.159 Angle : 0.668 13.945 15685 Z= 0.320 Chirality : 0.045 0.390 1868 Planarity : 0.004 0.081 1877 Dihedral : 8.507 59.816 1622 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.16 % Allowed : 16.86 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1351 helix: 1.02 (0.20), residues: 717 sheet: -0.88 (0.42), residues: 136 loop : -2.13 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 237 TYR 0.019 0.002 TYR D 19 PHE 0.035 0.002 PHE A 302 TRP 0.012 0.001 TRP B 165 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (11462) covalent geometry : angle 0.65508 / 0.32 (15615) SS BOND : bond 0.00321 / 0.17 ( 5) SS BOND : angle 1.16394 / 0.61 ( 10) hydrogen bonds : bond 0.04175 / 2.82 ( 545) hydrogen bonds : angle 4.09110 / 2.87 ( 1572) Misc. bond : bond 0.00180 / 0.09 ( 1) link_BETA1-3 : bond 0.00397 / 0.21 ( 1) link_BETA1-3 : angle 1.08416 / 0.70 ( 3) link_BETA1-4 : bond 0.00652 / 0.43 ( 7) link_BETA1-4 : angle 1.96124 / 1.29 ( 21) link_BETA1-6 : bond 0.00788 / 0.41 ( 1) link_BETA1-6 : angle 1.59720 / 1.23 ( 3) link_NAG-ASN : bond 0.00484 / 0.23 ( 11) link_NAG-ASN : angle 2.44345 / 1.85 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8727 (mptm) cc_final: 0.8344 (mppt) REVERT: A 75 VAL cc_start: 0.9230 (m) cc_final: 0.8877 (t) REVERT: A 80 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 186 GLU cc_start: 0.6998 (tp30) cc_final: 0.6503 (tm-30) REVERT: A 237 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: A 364 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: A 583 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7029 (ttt90) REVERT: A 598 ASP cc_start: 0.7884 (t0) cc_final: 0.7598 (m-30) REVERT: A 601 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: A 626 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8174 (ptp90) REVERT: A 657 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8586 (ptt-90) REVERT: B 165 TRP cc_start: 0.7337 (t60) cc_final: 0.7121 (t60) REVERT: B 248 LEU cc_start: 0.7609 (mt) cc_final: 0.7267 (tm) REVERT: B 259 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6716 (m) outliers start: 36 outliers final: 22 residues processed: 136 average time/residue: 0.6509 time to fit residues: 95.4573 Evaluate side-chains 136 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104153 restraints weight = 14101.041| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.15 r_work: 0.3006 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11488 Z= 0.176 Angle : 0.698 14.383 15685 Z= 0.333 Chirality : 0.045 0.389 1868 Planarity : 0.005 0.079 1877 Dihedral : 8.556 57.533 1622 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.34 % Allowed : 17.30 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.23), residues: 1351 helix: 0.99 (0.20), residues: 718 sheet: -0.85 (0.42), residues: 136 loop : -2.13 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.020 0.002 TYR D 19 PHE 0.036 0.002 PHE A 302 TRP 0.016 0.001 TRP A 257 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (11462) covalent geometry : angle 0.68431 / 0.33 (15615) SS BOND : bond 0.00341 / 0.17 ( 5) SS BOND : angle 1.22732 / 0.65 ( 10) hydrogen bonds : bond 0.04395 / 2.96 ( 545) hydrogen bonds : angle 4.11622 / 2.89 ( 1572) Misc. bond : bond 0.00188 / 0.10 ( 1) link_BETA1-3 : bond 0.00322 / 0.17 ( 1) link_BETA1-3 : angle 1.06071 / 0.66 ( 3) link_BETA1-4 : bond 0.00652 / 0.42 ( 7) link_BETA1-4 : angle 2.03880 / 1.34 ( 21) link_BETA1-6 : bond 0.00727 / 0.38 ( 1) link_BETA1-6 : angle 1.62206 / 1.27 ( 3) link_NAG-ASN : bond 0.00495 / 0.24 ( 11) link_NAG-ASN : angle 2.49993 / 1.90 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8706 (mptm) cc_final: 0.8298 (mppt) REVERT: A 75 VAL cc_start: 0.9241 (m) cc_final: 0.8898 (t) REVERT: A 80 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 114 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7513 (mtp180) REVERT: A 186 GLU cc_start: 0.6992 (tp30) cc_final: 0.6493 (tm-30) REVERT: A 237 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7598 (tp40) REVERT: A 364 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: A 583 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7034 (ttt90) REVERT: A 598 ASP cc_start: 0.7896 (t0) cc_final: 0.7589 (m-30) REVERT: A 601 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 626 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8299 (ptp90) REVERT: A 657 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8584 (ptt-90) REVERT: A 667 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7299 (tt0) REVERT: B 165 TRP cc_start: 0.7343 (t60) cc_final: 0.7130 (t60) REVERT: B 248 LEU cc_start: 0.7605 (mt) cc_final: 0.7258 (tm) REVERT: B 259 VAL cc_start: 0.7088 (OUTLIER) cc_final: 0.6718 (m) REVERT: C 180 ASP cc_start: 0.8550 (t70) cc_final: 0.8292 (t0) REVERT: C 237 ARG cc_start: 0.6961 (mmm160) cc_final: 0.6711 (mmm160) outliers start: 38 outliers final: 23 residues processed: 139 average time/residue: 0.5975 time to fit residues: 90.0431 Evaluate side-chains 139 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106965 restraints weight = 14292.491| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.20 r_work: 0.3067 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11488 Z= 0.124 Angle : 0.642 13.440 15685 Z= 0.305 Chirality : 0.043 0.390 1868 Planarity : 0.004 0.078 1877 Dihedral : 8.279 58.593 1622 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.63 % Allowed : 17.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1351 helix: 1.17 (0.20), residues: 718 sheet: -0.80 (0.42), residues: 136 loop : -2.03 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.017 0.001 TYR D 19 PHE 0.032 0.001 PHE A 302 TRP 0.018 0.001 TRP A 257 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11462) covalent geometry : angle 0.63082 / 0.30 (15615) SS BOND : bond 0.00279 / 0.15 ( 5) SS BOND : angle 0.91827 / 0.53 ( 10) hydrogen bonds : bond 0.03757 / 2.54 ( 545) hydrogen bonds : angle 4.03414 / 2.83 ( 1572) Misc. bond : bond 0.00153 / 0.08 ( 1) link_BETA1-3 : bond 0.00637 / 0.34 ( 1) link_BETA1-3 : angle 1.09371 / 0.80 ( 3) link_BETA1-4 : bond 0.00656 / 0.42 ( 7) link_BETA1-4 : angle 1.83516 / 1.20 ( 21) link_BETA1-6 : bond 0.00727 / 0.38 ( 1) link_BETA1-6 : angle 1.49081 / 1.12 ( 3) link_NAG-ASN : bond 0.00458 / 0.23 ( 11) link_NAG-ASN : angle 2.17673 / 1.64 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8681 (mptm) cc_final: 0.8288 (mppt) REVERT: A 75 VAL cc_start: 0.9208 (m) cc_final: 0.8847 (t) REVERT: A 114 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7477 (mtp180) REVERT: A 186 GLU cc_start: 0.7077 (tp30) cc_final: 0.6646 (tm-30) REVERT: A 231 MET cc_start: 0.8862 (tpt) cc_final: 0.8477 (mmm) REVERT: A 364 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: A 583 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7043 (ttt90) REVERT: A 598 ASP cc_start: 0.7816 (t0) cc_final: 0.7583 (m-30) REVERT: A 601 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 657 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8551 (ptt-90) REVERT: B 165 TRP cc_start: 0.7321 (t60) cc_final: 0.7114 (t60) REVERT: B 248 LEU cc_start: 0.7612 (mt) cc_final: 0.7256 (tm) REVERT: B 259 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6570 (m) outliers start: 30 outliers final: 22 residues processed: 133 average time/residue: 0.6074 time to fit residues: 87.4432 Evaluate side-chains 137 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107245 restraints weight = 14269.348| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.19 r_work: 0.3071 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11488 Z= 0.123 Angle : 0.637 13.701 15685 Z= 0.304 Chirality : 0.043 0.388 1868 Planarity : 0.004 0.076 1877 Dihedral : 8.172 59.032 1622 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.37 % Allowed : 18.35 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1351 helix: 1.24 (0.20), residues: 719 sheet: -0.64 (0.42), residues: 133 loop : -2.01 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 237 TYR 0.018 0.001 TYR D 19 PHE 0.031 0.001 PHE A 302 TRP 0.018 0.001 TRP A 257 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (11462) covalent geometry : angle 0.62674 / 0.30 (15615) SS BOND : bond 0.00268 / 0.14 ( 5) SS BOND : angle 0.91409 / 0.51 ( 10) hydrogen bonds : bond 0.03724 / 2.52 ( 545) hydrogen bonds : angle 4.03056 / 2.83 ( 1572) Misc. bond : bond 0.00149 / 0.08 ( 1) link_BETA1-3 : bond 0.00363 / 0.19 ( 1) link_BETA1-3 : angle 0.98890 / 0.67 ( 3) link_BETA1-4 : bond 0.00636 / 0.41 ( 7) link_BETA1-4 : angle 1.80946 / 1.19 ( 21) link_BETA1-6 : bond 0.00811 / 0.43 ( 1) link_BETA1-6 : angle 1.59526 / 1.22 ( 3) link_NAG-ASN : bond 0.00442 / 0.22 ( 11) link_NAG-ASN : angle 2.13270 / 1.60 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.64 seconds wall clock time: 75 minutes 58.95 seconds (4558.95 seconds total)