Starting phenix.real_space_refine on Fri Sep 11 20:39:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.map" model { file = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iyc_9751/09_2026/6iyc_9751.cif" } resolution = 2.6 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= 0.003 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 2 5.49 5 S 43 5.16 5 C 7236 2.51 5 N 1748 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 11037 Number of models: 1 Model: "" Number of chains: 14 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: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2407 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 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: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 226 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 11037 At special positions: 0 Unit cell: (109.1, 94.917, 134.193, 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 43 16.00 P 2 15.00 O 2008 8.00 N 1748 7.00 C 7236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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=2.01 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.02 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=2, 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 A 821 " - " ASN A 580 " " 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=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 512.2 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 59.6% alpha, 7.7% 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 Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.305A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.779A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.757A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.332A 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 153 through 157 removed outlier: 3.745A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.538A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.859A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.338A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.682A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.857A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.513A pdb=" N ARG A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 387 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.865A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.709A pdb=" N LEU A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.524A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.630A 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: 3.646A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (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 589 through 592 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.536A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 74 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.833A pdb=" N THR B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 108 " --> pdb=" O PHE B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.571A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.735A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.524A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.654A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 removed outlier: 4.209A pdb=" N ARG B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.606A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.006A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.639A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 30 through 61 removed outlier: 3.792A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.875A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 135 removed outlier: 3.510A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.914A pdb=" N LEU C 142 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 143 " --> pdb=" O ASP C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 143' Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.738A pdb=" N ALA C 166 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.627A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.804A 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: 3.504A 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 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 4.218A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.665A 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 43 removed outlier: 3.723A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 82 removed outlier: 4.083A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'E' and resid 14 through 26 removed outlier: 3.753A pdb=" N LEU E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.770A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 74 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.453A 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 412 through 414 removed outlier: 6.944A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.144A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.526A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.147A pdb=" N VAL E 34 " --> pdb=" O GLY B 382 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1674 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: 1.83 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1777 1.32 - 1.44: 3104 1.44 - 1.56: 6356 1.56 - 1.69: 7 1.69 - 1.81: 66 Bond restraints: 11310 Sorted by residual: bond pdb=" CB CYS A 248 " pdb=" SG CYS A 248 " ideal model delta sigma weight residual 1.808 1.694 0.114 3.30e-02 9.18e+02 1.20e+01 bond pdb=" C1 BMA G 5 " pdb=" C2 BMA G 5 " ideal model delta sigma weight residual 1.519 1.577 -0.058 2.00e-02 2.50e+03 8.50e+00 bond pdb=" C1 BMA G 5 " pdb=" O5 BMA G 5 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" CG LEU A 121 " pdb=" CD2 LEU A 121 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.90e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.45e+00 ... (remaining 11305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 14584 2.38 - 4.77: 704 4.77 - 7.15: 98 7.15 - 9.54: 33 9.54 - 11.92: 7 Bond angle restraints: 15426 Sorted by residual: angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" CB PRO B 117 " ideal model delta sigma weight residual 103.25 111.51 -8.26 1.05e+00 9.07e-01 6.19e+01 angle pdb=" C PRO A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.84 112.10 7.74 1.25e+00 6.40e-01 3.84e+01 angle pdb=" N ARG A 434 " pdb=" CA ARG A 434 " pdb=" C ARG A 434 " ideal model delta sigma weight residual 114.62 120.57 -5.95 1.14e+00 7.69e-01 2.72e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 109.81 120.48 -10.67 2.21e+00 2.05e-01 2.33e+01 angle pdb=" N TRP A 289 " pdb=" CA TRP A 289 " pdb=" C TRP A 289 " ideal model delta sigma weight residual 110.97 116.12 -5.15 1.09e+00 8.42e-01 2.23e+01 ... (remaining 15421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 6043 17.27 - 34.54: 299 34.54 - 51.81: 65 51.81 - 69.08: 7 69.08 - 86.35: 8 Dihedral angle restraints: 6422 sinusoidal: 2474 harmonic: 3948 Sorted by residual: 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 -172.35 86.35 1 1.00e+01 1.00e-02 8.99e+01 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 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -138.82 -41.18 0 5.00e+00 4.00e-02 6.78e+01 ... (remaining 6419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1607 0.095 - 0.190: 221 0.190 - 0.284: 28 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 1862 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 -2.02 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C1 NAG A 810 " pdb=" ND2 ASN A 387 " pdb=" C2 NAG A 810 " pdb=" O5 NAG A 810 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 562 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1859 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 580 " 0.040 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" CG ASN A 580 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 580 " -0.238 2.00e-02 2.50e+03 pdb=" ND2 ASN A 580 " 0.439 2.00e-02 2.50e+03 pdb=" C1 NAG A 821 " -0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 387 " -0.055 2.00e-02 2.50e+03 6.25e-02 4.88e+01 pdb=" CG ASN A 387 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 387 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 387 " 0.093 2.00e-02 2.50e+03 pdb=" C1 NAG A 810 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 810 " 0.050 2.00e-02 2.50e+03 4.06e-02 2.06e+01 pdb=" C7 NAG A 810 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG A 810 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG A 810 " -0.064 2.00e-02 2.50e+03 pdb=" O7 NAG A 810 " -0.010 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 87 2.62 - 3.19: 9180 3.19 - 3.76: 16760 3.76 - 4.33: 23330 4.33 - 4.90: 38431 Nonbonded interactions: 87788 Sorted by model distance: nonbonded pdb=" O3 NAG A 810 " pdb=" O7 NAG A 810 " model vdw 2.053 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 100 " pdb=" OH TYR A 457 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 286 " pdb=" O VAL A 291 " model vdw 2.281 3.040 ... (remaining 87783 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 : 0.011 0.114 11337 Z= 0.469 Angle : 1.240 17.647 15497 Z= 0.623 Chirality : 0.070 0.474 1862 Planarity : 0.008 0.079 1860 Dihedral : 11.412 83.173 3864 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.46 % Favored : 92.32 % Rotamer: Outliers : 0.88 % Allowed : 3.68 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.39 % Twisted General : 0.54 % 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: -3.74 (0.18), residues: 1341 helix: -2.11 (0.15), residues: 723 sheet: -1.59 (0.45), residues: 115 loop : -3.09 (0.21), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 432 TYR 0.036 0.004 TYR C 90 PHE 0.050 0.005 PHE A 448 TRP 0.054 0.005 TRP C 227 HIS 0.020 0.005 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.01124 / 0.47 (11310) covalent geometry : angle 1.19627 / 0.61 (15426) SS BOND : bond 0.01117 / 0.56 ( 4) SS BOND : angle 2.86139 / 1.65 ( 8) hydrogen bonds : bond 0.18117 / 11.83 ( 587) hydrogen bonds : angle 6.58638 / 4.58 ( 1674) Misc. bond : bond 0.00237 / 0.12 ( 2) link_BETA1-3 : bond 0.01258 / 0.66 ( 1) link_BETA1-3 : angle 0.97003 / 0.72 ( 3) link_BETA1-4 : bond 0.00758 / 0.47 ( 7) link_BETA1-4 : angle 3.21341 / 2.01 ( 21) link_BETA1-6 : bond 0.00614 / 0.32 ( 1) link_BETA1-6 : angle 1.29000 / 0.78 ( 3) link_NAG-ASN : bond 0.02946 / 2.07 ( 12) link_NAG-ASN : angle 6.40460 / 4.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9133 (mmp) cc_final: 0.8554 (mmm) REVERT: A 617 LEU cc_start: 0.8875 (mt) cc_final: 0.8642 (mt) REVERT: A 650 GLU cc_start: 0.8429 (tt0) cc_final: 0.8002 (tt0) REVERT: B 84 MET cc_start: 0.8629 (mtt) cc_final: 0.8329 (mtp) REVERT: B 248 LEU cc_start: 0.8831 (mt) cc_final: 0.8555 (mp) REVERT: B 252 VAL cc_start: 0.8996 (t) cc_final: 0.8613 (m) REVERT: B 255 VAL cc_start: 0.9113 (t) cc_final: 0.8900 (m) REVERT: C 180 ASP cc_start: 0.8414 (t70) cc_final: 0.8172 (t0) REVERT: D 39 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7492 (tpp80) REVERT: E 1 LEU cc_start: 0.8511 (tp) cc_final: 0.8279 (tp) outliers start: 10 outliers final: 7 residues processed: 256 average time/residue: 0.6103 time to fit residues: 168.5011 Evaluate side-chains 146 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 142 ASN A 158 HIS A 163 GLN A 305 GLN A 358 ASN A 454 GLN A 531 ASN A 606 GLN B 214 HIS B 222 GLN C 116 GLN D 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088017 restraints weight = 16680.233| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.26 r_work: 0.2994 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11337 Z= 0.171 Angle : 0.767 11.169 15497 Z= 0.373 Chirality : 0.049 0.368 1862 Planarity : 0.005 0.057 1860 Dihedral : 8.032 71.938 1541 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 4.04 % Allowed : 11.14 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.16 % 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: -1.62 (0.22), residues: 1341 helix: -0.04 (0.19), residues: 728 sheet: -1.60 (0.43), residues: 126 loop : -2.48 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 114 TYR 0.018 0.002 TYR A 569 PHE 0.035 0.002 PHE A 302 TRP 0.015 0.002 TRP C 209 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11310) covalent geometry : angle 0.74718 / 0.37 (15426) SS BOND : bond 0.00324 / 0.16 ( 4) SS BOND : angle 1.63364 / 0.96 ( 8) hydrogen bonds : bond 0.05236 / 3.47 ( 587) hydrogen bonds : angle 4.48575 / 3.09 ( 1674) Misc. bond : bond 0.00861 / 0.45 ( 2) link_BETA1-3 : bond 0.00650 / 0.34 ( 1) link_BETA1-3 : angle 0.54454 / 0.40 ( 3) link_BETA1-4 : bond 0.00660 / 0.36 ( 7) link_BETA1-4 : angle 1.62911 / 1.07 ( 21) link_BETA1-6 : bond 0.01305 / 0.69 ( 1) link_BETA1-6 : angle 1.40582 / 1.10 ( 3) link_NAG-ASN : bond 0.00630 / 0.37 ( 12) link_NAG-ASN : angle 3.38322 / 2.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.441 Fit side-chains REVERT: A 231 MET cc_start: 0.9224 (mmp) cc_final: 0.8879 (mmm) REVERT: A 237 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6952 (tm-30) REVERT: A 317 ASP cc_start: 0.7455 (t70) cc_final: 0.7018 (t0) REVERT: A 364 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: A 540 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: A 617 LEU cc_start: 0.8759 (mt) cc_final: 0.8474 (mt) REVERT: B 84 MET cc_start: 0.8917 (mtt) cc_final: 0.8609 (mtp) REVERT: B 146 MET cc_start: 0.7295 (tpt) cc_final: 0.7026 (tpt) REVERT: B 153 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 165 TRP cc_start: 0.8851 (t60) cc_final: 0.8530 (t60) REVERT: B 252 VAL cc_start: 0.9023 (t) cc_final: 0.8724 (m) REVERT: C 240 GLN cc_start: 0.8485 (mt0) cc_final: 0.8218 (mm-40) REVERT: D 8 ASN cc_start: 0.8153 (p0) cc_final: 0.7917 (p0) REVERT: D 39 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7607 (tpp80) REVERT: D 40 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 91 TYR cc_start: 0.8798 (m-80) cc_final: 0.8441 (m-80) outliers start: 46 outliers final: 12 residues processed: 187 average time/residue: 0.5661 time to fit residues: 114.7935 Evaluate side-chains 151 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN A 385 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087180 restraints weight = 16725.365| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.29 r_work: 0.2986 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11337 Z= 0.150 Angle : 0.689 10.537 15497 Z= 0.334 Chirality : 0.047 0.522 1862 Planarity : 0.005 0.056 1860 Dihedral : 7.410 67.187 1538 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 3.86 % Allowed : 13.77 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -0.67 (0.23), residues: 1341 helix: 0.90 (0.20), residues: 714 sheet: -1.26 (0.44), residues: 128 loop : -2.24 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.016 0.002 TYR A 569 PHE 0.033 0.002 PHE A 302 TRP 0.016 0.001 TRP D 58 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11310) covalent geometry : angle 0.67331 / 0.33 (15426) SS BOND : bond 0.00355 / 0.18 ( 4) SS BOND : angle 1.17939 / 0.69 ( 8) hydrogen bonds : bond 0.04538 / 3.00 ( 587) hydrogen bonds : angle 4.15813 / 2.86 ( 1674) Misc. bond : bond 0.00460 / 0.24 ( 2) link_BETA1-3 : bond 0.00771 / 0.41 ( 1) link_BETA1-3 : angle 0.57916 / 0.41 ( 3) link_BETA1-4 : bond 0.00404 / 0.25 ( 7) link_BETA1-4 : angle 1.66070 / 1.10 ( 21) link_BETA1-6 : bond 0.00984 / 0.52 ( 1) link_BETA1-6 : angle 1.53088 / 1.17 ( 3) link_NAG-ASN : bond 0.00548 / 0.32 ( 12) link_NAG-ASN : angle 2.77694 / 2.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9236 (mmp) cc_final: 0.8812 (mmm) REVERT: A 237 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 317 ASP cc_start: 0.7514 (t70) cc_final: 0.7051 (t0) REVERT: A 617 LEU cc_start: 0.8769 (mt) cc_final: 0.8482 (mt) REVERT: B 84 MET cc_start: 0.8943 (mtt) cc_final: 0.8628 (mtp) REVERT: B 146 MET cc_start: 0.7229 (tpt) cc_final: 0.6958 (tpt) REVERT: B 252 VAL cc_start: 0.9015 (t) cc_final: 0.8756 (m) REVERT: C 109 ARG cc_start: 0.6783 (pmm150) cc_final: 0.6568 (pmm150) REVERT: C 240 GLN cc_start: 0.8516 (mt0) cc_final: 0.8162 (mm110) REVERT: D 8 ASN cc_start: 0.8067 (p0) cc_final: 0.7712 (p0) REVERT: D 39 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7529 (tpp80) REVERT: D 58 TRP cc_start: 0.7291 (OUTLIER) cc_final: 0.7072 (t60) REVERT: D 91 TYR cc_start: 0.8794 (m-80) cc_final: 0.8363 (m-80) outliers start: 44 outliers final: 19 residues processed: 173 average time/residue: 0.5541 time to fit residues: 104.3607 Evaluate side-chains 155 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 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 561 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088136 restraints weight = 16790.885| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.31 r_work: 0.3000 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11337 Z= 0.126 Angle : 0.656 10.399 15497 Z= 0.317 Chirality : 0.045 0.406 1862 Planarity : 0.004 0.053 1860 Dihedral : 7.117 66.966 1538 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 4.12 % Allowed : 14.39 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -0.14 (0.23), residues: 1341 helix: 1.39 (0.20), residues: 713 sheet: -1.10 (0.45), residues: 124 loop : -2.05 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 583 TYR 0.015 0.001 TYR A 569 PHE 0.032 0.001 PHE A 302 TRP 0.014 0.001 TRP C 209 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (11310) covalent geometry : angle 0.64416 / 0.31 (15426) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 0.95622 / 0.56 ( 8) hydrogen bonds : bond 0.04055 / 2.68 ( 587) hydrogen bonds : angle 4.01885 / 2.76 ( 1674) Misc. bond : bond 0.00291 / 0.15 ( 2) link_BETA1-3 : bond 0.00677 / 0.36 ( 1) link_BETA1-3 : angle 0.73243 / 0.54 ( 3) link_BETA1-4 : bond 0.00422 / 0.25 ( 7) link_BETA1-4 : angle 1.47276 / 0.96 ( 21) link_BETA1-6 : bond 0.00912 / 0.48 ( 1) link_BETA1-6 : angle 1.58386 / 1.20 ( 3) link_NAG-ASN : bond 0.00504 / 0.29 ( 12) link_NAG-ASN : angle 2.42091 / 1.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.9226 (mmp) cc_final: 0.8784 (mmm) REVERT: B 84 MET cc_start: 0.8946 (mtt) cc_final: 0.8633 (mtp) REVERT: B 146 MET cc_start: 0.7361 (tpt) cc_final: 0.7118 (tpt) REVERT: B 149 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 252 VAL cc_start: 0.9004 (t) cc_final: 0.8738 (m) REVERT: C 187 TYR cc_start: 0.8372 (m-80) cc_final: 0.7994 (m-10) REVERT: C 240 GLN cc_start: 0.8579 (mt0) cc_final: 0.8239 (mm-40) REVERT: D 8 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7724 (p0) REVERT: D 39 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7503 (tpp80) REVERT: D 58 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6800 (t60) outliers start: 47 outliers final: 22 residues processed: 175 average time/residue: 0.5779 time to fit residues: 109.7667 Evaluate side-chains 156 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 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 561 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088148 restraints weight = 16748.319| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.31 r_work: 0.2999 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11337 Z= 0.122 Angle : 0.642 10.300 15497 Z= 0.310 Chirality : 0.044 0.371 1862 Planarity : 0.004 0.048 1860 Dihedral : 6.932 66.278 1537 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 3.42 % Allowed : 15.61 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.17 (0.23), residues: 1341 helix: 1.62 (0.20), residues: 717 sheet: -0.91 (0.47), residues: 124 loop : -1.93 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.014 0.001 TYR D 47 PHE 0.030 0.001 PHE A 302 TRP 0.013 0.001 TRP C 209 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11310) covalent geometry : angle 0.63083 / 0.31 (15426) SS BOND : bond 0.00275 / 0.14 ( 4) SS BOND : angle 0.91109 / 0.53 ( 8) hydrogen bonds : bond 0.03862 / 2.56 ( 587) hydrogen bonds : angle 3.94570 / 2.71 ( 1674) Misc. bond : bond 0.00228 / 0.12 ( 2) link_BETA1-3 : bond 0.00671 / 0.35 ( 1) link_BETA1-3 : angle 0.71205 / 0.52 ( 3) link_BETA1-4 : bond 0.00348 / 0.20 ( 7) link_BETA1-4 : angle 1.45530 / 0.94 ( 21) link_BETA1-6 : bond 0.01078 / 0.57 ( 1) link_BETA1-6 : angle 1.73657 / 1.32 ( 3) link_NAG-ASN : bond 0.00490 / 0.29 ( 12) link_NAG-ASN : angle 2.27402 / 1.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8613 (mppt) REVERT: A 96 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (t) REVERT: A 138 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.8932 (m) REVERT: A 231 MET cc_start: 0.9221 (mmp) cc_final: 0.8765 (mmm) REVERT: B 84 MET cc_start: 0.8928 (mtt) cc_final: 0.8607 (mtp) REVERT: B 149 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 248 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 252 VAL cc_start: 0.8999 (t) cc_final: 0.8739 (m) REVERT: C 109 ARG cc_start: 0.6848 (pmm150) cc_final: 0.6614 (pmm150) REVERT: C 187 TYR cc_start: 0.8402 (m-80) cc_final: 0.8105 (m-10) REVERT: C 240 GLN cc_start: 0.8569 (mt0) cc_final: 0.8228 (mm-40) REVERT: D 8 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7728 (p0) REVERT: D 39 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7486 (tpp80) REVERT: D 58 TRP cc_start: 0.7053 (OUTLIER) cc_final: 0.6761 (t60) REVERT: E 25 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7444 (pt) outliers start: 39 outliers final: 18 residues processed: 165 average time/residue: 0.5719 time to fit residues: 102.4222 Evaluate side-chains 158 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 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 603 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087260 restraints weight = 16681.127| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.29 r_work: 0.2986 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11337 Z= 0.147 Angle : 0.666 10.253 15497 Z= 0.322 Chirality : 0.045 0.371 1862 Planarity : 0.004 0.052 1860 Dihedral : 6.987 65.711 1537 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 3.51 % Allowed : 16.14 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.23 (0.24), residues: 1341 helix: 1.64 (0.20), residues: 720 sheet: -0.77 (0.47), residues: 127 loop : -1.92 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 583 TYR 0.015 0.001 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11310) covalent geometry : angle 0.65444 / 0.32 (15426) SS BOND : bond 0.00340 / 0.17 ( 4) SS BOND : angle 0.99702 / 0.58 ( 8) hydrogen bonds : bond 0.04115 / 2.71 ( 587) hydrogen bonds : angle 3.94632 / 2.71 ( 1674) Misc. bond : bond 0.00235 / 0.12 ( 2) link_BETA1-3 : bond 0.00728 / 0.38 ( 1) link_BETA1-3 : angle 0.61513 / 0.41 ( 3) link_BETA1-4 : bond 0.00354 / 0.21 ( 7) link_BETA1-4 : angle 1.56282 / 1.00 ( 21) link_BETA1-6 : bond 0.00986 / 0.52 ( 1) link_BETA1-6 : angle 1.63189 / 1.25 ( 3) link_NAG-ASN : bond 0.00518 / 0.30 ( 12) link_NAG-ASN : angle 2.37638 / 1.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8619 (mppt) REVERT: A 138 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.8907 (m) REVERT: A 231 MET cc_start: 0.9186 (mmp) cc_final: 0.8684 (mmm) REVERT: A 317 ASP cc_start: 0.7473 (t70) cc_final: 0.7048 (t0) REVERT: A 597 LYS cc_start: 0.8844 (tmmm) cc_final: 0.8540 (tmtm) REVERT: B 84 MET cc_start: 0.8923 (mtt) cc_final: 0.8588 (mtp) REVERT: B 149 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7606 (mp) REVERT: B 252 VAL cc_start: 0.9016 (t) cc_final: 0.8762 (m) REVERT: B 273 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6550 (pt0) REVERT: C 187 TYR cc_start: 0.8398 (m-80) cc_final: 0.7944 (m-10) REVERT: C 240 GLN cc_start: 0.8592 (mt0) cc_final: 0.8245 (mm-40) REVERT: D 8 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7756 (p0) REVERT: D 39 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7498 (tpp80) REVERT: D 47 TYR cc_start: 0.6587 (t80) cc_final: 0.6266 (t80) REVERT: D 58 TRP cc_start: 0.6972 (OUTLIER) cc_final: 0.6671 (t60) REVERT: E 25 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7286 (pt) outliers start: 40 outliers final: 23 residues processed: 167 average time/residue: 0.5566 time to fit residues: 101.0116 Evaluate side-chains 161 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET 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 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088391 restraints weight = 16664.131| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.29 r_work: 0.3006 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11337 Z= 0.124 Angle : 0.646 10.181 15497 Z= 0.311 Chirality : 0.044 0.369 1862 Planarity : 0.004 0.049 1860 Dihedral : 6.896 65.743 1537 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 3.07 % Allowed : 17.37 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.42 (0.24), residues: 1341 helix: 1.81 (0.20), residues: 718 sheet: -0.68 (0.47), residues: 127 loop : -1.84 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.014 0.001 TYR D 47 PHE 0.030 0.001 PHE A 302 TRP 0.011 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (11310) covalent geometry : angle 0.63589 / 0.31 (15426) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 0.85618 / 0.51 ( 8) hydrogen bonds : bond 0.03826 / 2.54 ( 587) hydrogen bonds : angle 3.90340 / 2.68 ( 1674) Misc. bond : bond 0.00217 / 0.11 ( 2) link_BETA1-3 : bond 0.00670 / 0.35 ( 1) link_BETA1-3 : angle 0.73162 / 0.54 ( 3) link_BETA1-4 : bond 0.00391 / 0.23 ( 7) link_BETA1-4 : angle 1.43745 / 0.90 ( 21) link_BETA1-6 : bond 0.00905 / 0.48 ( 1) link_BETA1-6 : angle 1.63468 / 1.25 ( 3) link_NAG-ASN : bond 0.00495 / 0.29 ( 12) link_NAG-ASN : angle 2.20053 / 1.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8613 (mppt) REVERT: A 138 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8917 (m) REVERT: A 231 MET cc_start: 0.9186 (mmp) cc_final: 0.8711 (mmm) REVERT: A 317 ASP cc_start: 0.7456 (t70) cc_final: 0.7046 (t0) REVERT: A 597 LYS cc_start: 0.8847 (tmmm) cc_final: 0.8539 (tmtm) REVERT: B 84 MET cc_start: 0.8932 (mtt) cc_final: 0.8591 (mtp) REVERT: B 149 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 248 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 252 VAL cc_start: 0.8994 (t) cc_final: 0.8749 (m) REVERT: C 109 ARG cc_start: 0.6824 (pmm150) cc_final: 0.6581 (pmm150) REVERT: C 187 TYR cc_start: 0.8347 (m-80) cc_final: 0.7956 (m-10) REVERT: C 214 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7064 (mm) REVERT: C 240 GLN cc_start: 0.8573 (mt0) cc_final: 0.8222 (mm-40) REVERT: D 8 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7728 (p0) REVERT: D 39 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7496 (tpp80) REVERT: D 58 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6568 (t60) REVERT: E 25 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7282 (pt) outliers start: 35 outliers final: 18 residues processed: 163 average time/residue: 0.5629 time to fit residues: 99.5755 Evaluate side-chains 157 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086647 restraints weight = 16551.493| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.30 r_work: 0.2971 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11337 Z= 0.162 Angle : 0.686 10.167 15497 Z= 0.331 Chirality : 0.046 0.371 1862 Planarity : 0.004 0.051 1860 Dihedral : 7.027 64.749 1537 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 3.07 % Allowed : 17.54 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.42 (0.24), residues: 1341 helix: 1.81 (0.20), residues: 718 sheet: -0.74 (0.47), residues: 127 loop : -1.81 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 543 TYR 0.015 0.001 TYR A 173 PHE 0.029 0.002 PHE A 302 TRP 0.011 0.001 TRP D 58 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11310) covalent geometry : angle 0.67418 / 0.33 (15426) SS BOND : bond 0.00355 / 0.18 ( 4) SS BOND : angle 1.01872 / 0.60 ( 8) hydrogen bonds : bond 0.04202 / 2.77 ( 587) hydrogen bonds : angle 3.95302 / 2.71 ( 1674) Misc. bond : bond 0.00235 / 0.12 ( 2) link_BETA1-3 : bond 0.00733 / 0.39 ( 1) link_BETA1-3 : angle 0.51108 / 0.35 ( 3) link_BETA1-4 : bond 0.00313 / 0.19 ( 7) link_BETA1-4 : angle 1.60179 / 1.02 ( 21) link_BETA1-6 : bond 0.01001 / 0.53 ( 1) link_BETA1-6 : angle 1.59498 / 1.22 ( 3) link_NAG-ASN : bond 0.00543 / 0.31 ( 12) link_NAG-ASN : angle 2.39654 / 1.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8643 (mppt) REVERT: A 138 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.8950 (m) REVERT: A 231 MET cc_start: 0.9217 (mmp) cc_final: 0.8888 (tpt) REVERT: A 317 ASP cc_start: 0.7488 (t70) cc_final: 0.7082 (t0) REVERT: A 597 LYS cc_start: 0.8915 (tmmm) cc_final: 0.8671 (tmtm) REVERT: B 84 MET cc_start: 0.8951 (mtt) cc_final: 0.8613 (mtp) REVERT: B 149 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 248 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 252 VAL cc_start: 0.9002 (t) cc_final: 0.8752 (m) REVERT: B 273 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6588 (pt0) REVERT: C 187 TYR cc_start: 0.8269 (m-80) cc_final: 0.7889 (m-10) REVERT: C 214 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7236 (mm) REVERT: C 224 MET cc_start: 0.8772 (tpp) cc_final: 0.8026 (mpp) REVERT: C 240 GLN cc_start: 0.8576 (mt0) cc_final: 0.8238 (mm-40) REVERT: D 8 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7776 (p0) REVERT: D 39 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7513 (tpp80) REVERT: D 58 TRP cc_start: 0.6949 (OUTLIER) cc_final: 0.6723 (t60) REVERT: E 25 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7286 (pt) outliers start: 35 outliers final: 23 residues processed: 164 average time/residue: 0.5845 time to fit residues: 103.9665 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 MET 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 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 123 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088025 restraints weight = 16471.499| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.25 r_work: 0.2999 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11337 Z= 0.134 Angle : 0.664 11.481 15497 Z= 0.319 Chirality : 0.045 0.368 1862 Planarity : 0.004 0.050 1860 Dihedral : 6.946 64.549 1537 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.72 % Allowed : 18.07 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.54 (0.24), residues: 1341 helix: 1.88 (0.20), residues: 719 sheet: -0.68 (0.48), residues: 127 loop : -1.72 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.014 0.001 TYR A 569 PHE 0.031 0.001 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11310) covalent geometry : angle 0.65397 / 0.32 (15426) SS BOND : bond 0.00275 / 0.14 ( 4) SS BOND : angle 0.88155 / 0.52 ( 8) hydrogen bonds : bond 0.03913 / 2.59 ( 587) hydrogen bonds : angle 3.93717 / 2.71 ( 1674) Misc. bond : bond 0.00221 / 0.12 ( 2) link_BETA1-3 : bond 0.00676 / 0.36 ( 1) link_BETA1-3 : angle 0.65769 / 0.49 ( 3) link_BETA1-4 : bond 0.00348 / 0.20 ( 7) link_BETA1-4 : angle 1.48238 / 0.96 ( 21) link_BETA1-6 : bond 0.00898 / 0.47 ( 1) link_BETA1-6 : angle 1.59835 / 1.22 ( 3) link_NAG-ASN : bond 0.00495 / 0.29 ( 12) link_NAG-ASN : angle 2.22290 / 1.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8619 (mppt) REVERT: A 138 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.8915 (m) REVERT: A 231 MET cc_start: 0.9173 (mmp) cc_final: 0.8853 (mmm) REVERT: A 317 ASP cc_start: 0.7480 (t70) cc_final: 0.7061 (t0) REVERT: A 543 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: A 591 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8276 (mmmm) REVERT: A 597 LYS cc_start: 0.8897 (tmmm) cc_final: 0.8671 (tmtm) REVERT: B 84 MET cc_start: 0.8922 (mtt) cc_final: 0.8573 (mtp) REVERT: B 248 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 252 VAL cc_start: 0.8959 (t) cc_final: 0.8602 (m) REVERT: C 99 GLU cc_start: 0.7751 (tt0) cc_final: 0.7031 (pt0) REVERT: C 187 TYR cc_start: 0.8189 (m-80) cc_final: 0.7891 (m-10) REVERT: C 214 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7124 (mm) REVERT: C 240 GLN cc_start: 0.8561 (mt0) cc_final: 0.8221 (mm-40) REVERT: D 8 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7681 (p0) REVERT: D 39 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7488 (tpp80) REVERT: D 58 TRP cc_start: 0.6940 (OUTLIER) cc_final: 0.6707 (t60) REVERT: E 25 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7327 (pt) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 0.5898 time to fit residues: 100.9385 Evaluate side-chains 157 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089900 restraints weight = 16606.144| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.29 r_work: 0.3030 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11337 Z= 0.111 Angle : 0.638 11.026 15497 Z= 0.307 Chirality : 0.043 0.368 1862 Planarity : 0.004 0.050 1860 Dihedral : 6.750 63.587 1537 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 2.11 % Allowed : 18.86 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.66 (0.24), residues: 1341 helix: 1.99 (0.20), residues: 720 sheet: -0.62 (0.48), residues: 127 loop : -1.68 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.013 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11310) covalent geometry : angle 0.62912 / 0.31 (15426) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.69677 / 0.41 ( 8) hydrogen bonds : bond 0.03485 / 2.32 ( 587) hydrogen bonds : angle 3.89187 / 2.68 ( 1674) Misc. bond : bond 0.00199 / 0.10 ( 2) link_BETA1-3 : bond 0.00633 / 0.33 ( 1) link_BETA1-3 : angle 0.80896 / 0.63 ( 3) link_BETA1-4 : bond 0.00419 / 0.24 ( 7) link_BETA1-4 : angle 1.34754 / 0.87 ( 21) link_BETA1-6 : bond 0.00901 / 0.47 ( 1) link_BETA1-6 : angle 1.64687 / 1.26 ( 3) link_NAG-ASN : bond 0.00460 / 0.27 ( 12) link_NAG-ASN : angle 2.02423 / 1.44 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 138 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8900 (m) REVERT: A 231 MET cc_start: 0.9156 (mmp) cc_final: 0.8785 (tpt) REVERT: A 543 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8082 (mtm-85) REVERT: A 591 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8325 (mmmm) REVERT: B 84 MET cc_start: 0.8864 (mtt) cc_final: 0.8526 (mtp) REVERT: B 146 MET cc_start: 0.7070 (ttp) cc_final: 0.6617 (tpp) REVERT: B 248 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 252 VAL cc_start: 0.8922 (t) cc_final: 0.8670 (m) REVERT: B 273 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6559 (pt0) REVERT: C 99 GLU cc_start: 0.7734 (tt0) cc_final: 0.7018 (pt0) REVERT: C 187 TYR cc_start: 0.8134 (m-80) cc_final: 0.7894 (m-10) REVERT: C 240 GLN cc_start: 0.8523 (mt0) cc_final: 0.8148 (mm-40) REVERT: D 8 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7686 (p0) REVERT: D 39 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7366 (tpp80) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 0.5994 time to fit residues: 99.6720 Evaluate side-chains 144 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 130 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088924 restraints weight = 16782.112| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.31 r_work: 0.3009 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11337 Z= 0.122 Angle : 0.654 10.401 15497 Z= 0.314 Chirality : 0.044 0.398 1862 Planarity : 0.004 0.085 1860 Dihedral : 6.746 62.293 1537 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.58 % Allowed : 19.56 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: 0.70 (0.24), residues: 1341 helix: 2.04 (0.20), residues: 718 sheet: -0.63 (0.48), residues: 127 loop : -1.69 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 114 TYR 0.027 0.001 TYR B 77 PHE 0.028 0.001 PHE A 302 TRP 0.023 0.001 TRP D 58 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11310) covalent geometry : angle 0.64539 / 0.31 (15426) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 0.80543 / 0.47 ( 8) hydrogen bonds : bond 0.03597 / 2.39 ( 587) hydrogen bonds : angle 3.86942 / 2.66 ( 1674) Misc. bond : bond 0.00297 / 0.16 ( 2) link_BETA1-3 : bond 0.00644 / 0.34 ( 1) link_BETA1-3 : angle 0.74490 / 0.56 ( 3) link_BETA1-4 : bond 0.00385 / 0.23 ( 7) link_BETA1-4 : angle 1.40519 / 0.89 ( 21) link_BETA1-6 : bond 0.00927 / 0.49 ( 1) link_BETA1-6 : angle 1.62865 / 1.25 ( 3) link_NAG-ASN : bond 0.00447 / 0.26 ( 12) link_NAG-ASN : angle 2.06641 / 1.48 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5041.26 seconds wall clock time: 86 minutes 35.73 seconds (5195.73 seconds total)