Starting phenix.real_space_refine on Fri Jul 3 11:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.map" model { file = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8avg_15682/07_2026/8avg_15682.cif" } resolution = 4.01 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= 0.001 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 Fe 4 7.16 5 S 89 5.16 5 C 8712 2.51 5 N 2400 2.21 5 O 2541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4720 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 9 Chain: "B" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5494 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 28, 'TRANS': 665} Chain breaks: 6 Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3497 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 2 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10320 SG CYS C 99 46.109 48.121 84.283 1.00 35.37 S ATOM 10421 SG CYS C 112 51.785 48.553 81.278 1.00 47.71 S ATOM 10395 SG CYS C 109 46.698 46.131 78.253 1.00 46.71 S Time building chain proxies: 3.02, per 1000 atoms: 0.22 Number of scatterers: 13746 At special positions: 0 Unit cell: (79.98, 113.52, 156.52, 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) Fe 4 26.01 S 89 16.00 O 2541 8.00 N 2400 7.00 C 8712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 572.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 109 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 99 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 112 " Number of angles added : 9 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 37 sheets defined 11.7% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.063A pdb=" N PHE A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 159 " --> pdb=" O GLY A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.802A pdb=" N GLU B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 4.246A pdb=" N VAL B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 554 Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.956A pdb=" N SER C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.518A pdb=" N GLN C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.005A pdb=" N LEU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 removed outlier: 3.559A pdb=" N ARG C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 264 through 276 removed outlier: 3.549A pdb=" N CYS C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 307 removed outlier: 3.622A pdb=" N ILE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.518A pdb=" N SER C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 382 through 395 removed outlier: 3.636A pdb=" N LEU C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.820A pdb=" N THR A 376 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.571A pdb=" N PHE A 12 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 368 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 27 removed outlier: 3.929A pdb=" N CYS A 23 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 76 removed outlier: 3.893A pdb=" N THR A 87 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 117 removed outlier: 7.013A pdb=" N ALA A 127 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N MET A 115 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 125 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP A 117 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 123 " --> pdb=" O TRP A 117 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 144 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR A 137 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 142 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 200 Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246 removed outlier: 4.108A pdb=" N ALA A 245 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.615A pdb=" N VAL A 265 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS A 277 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A 267 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 294 removed outlier: 6.503A pdb=" N TRP A 304 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 292 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 302 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 301 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR A 324 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 332 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 378 through 379 removed outlier: 4.449A pdb=" N ASP A 378 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 399 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG A 417 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 401 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 424 through 429 removed outlier: 6.567A pdb=" N LEU A 440 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 427 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 438 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AB4, first strand: chain 'A' and resid 519 through 520 Processing sheet with id=AB5, first strand: chain 'A' and resid 558 through 561 removed outlier: 6.682A pdb=" N GLN A 573 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 572 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 579 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 610 through 616 removed outlier: 4.055A pdb=" N ALA A 639 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 633 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 645 through 648 removed outlier: 3.614A pdb=" N ARG A 690 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 697 through 701 removed outlier: 4.684A pdb=" N ILE A 709 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 12 removed outlier: 5.671A pdb=" N VAL B 8 " --> pdb=" O ARG B 825 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG B 825 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 821 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 812 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 815 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG B 782 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.499A pdb=" N GLY B 81 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 64 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 79 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TRP B 66 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU B 77 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 99 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.550A pdb=" N ILE B 116 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 128 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 139 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR B 154 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 152 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.719A pdb=" N CYS B 166 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 181 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 178 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 187 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 202 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 189 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 210 through 218 removed outlier: 6.432A pdb=" N CYS B 227 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 213 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 225 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP B 215 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B 223 " --> pdb=" O TRP B 215 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR B 217 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 285 through 289 removed outlier: 3.546A pdb=" N ALA B 287 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 318 removed outlier: 3.562A pdb=" N LEU B 317 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 331 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 343 through 348 removed outlier: 6.295A pdb=" N HIS B 358 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS B 346 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 356 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 348 " --> pdb=" O MET B 354 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N MET B 354 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 390 through 395 removed outlier: 7.023A pdb=" N THR B 405 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 393 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE B 403 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 413 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 429 " --> pdb=" O TRP B 417 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 443 through 450 removed outlier: 6.408A pdb=" N GLN B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 570 through 575 removed outlier: 7.042A pdb=" N ALA B 585 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 573 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 583 " --> pdb=" O VAL B 573 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.555A pdb=" N LEU B 598 " --> pdb=" O GLN B 608 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 608 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 619 through 622 Processing sheet with id=AD6, first strand: chain 'B' and resid 672 through 676 removed outlier: 4.528A pdb=" N SER B 688 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 695 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER B 715 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY B 697 " --> pdb=" O CYS B 713 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS B 713 " --> pdb=" O GLY B 697 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 723 through 728 removed outlier: 6.495A pdb=" N GLY B 743 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 726 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 741 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 728 " --> pdb=" O ILE B 739 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE B 739 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 88 through 91 removed outlier: 3.586A pdb=" N ALA C 88 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 166 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 165 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 218 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE C 167 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 220 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG C 242 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 218 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU C 244 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 220 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY C 246 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS C 280 " --> pdb=" O ARG C 242 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU C 244 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 282 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY C 246 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS C 284 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 314 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 317 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 421 through 425 removed outlier: 3.704A pdb=" N ALA C 429 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 421 through 425 removed outlier: 5.169A pdb=" N TRP C 433 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY C 449 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP C 441 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C 447 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE C 448 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL C 477 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 450 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU C 475 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG C 452 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER C 470 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE C 521 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C 472 " --> pdb=" O ILE C 521 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 5982 1.43 - 1.64: 7956 1.64 - 1.85: 117 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 14067 Sorted by residual: bond pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N ILE A 15 " pdb=" CA ILE A 15 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.04e+00 bond pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.48e+00 bond pdb=" N ARG A 48 " pdb=" CA ARG A 48 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 7.82e+00 bond pdb=" N GLN B 126 " pdb=" CA GLN B 126 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.76e+00 ... (remaining 14062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 18214 1.49 - 2.98: 727 2.98 - 4.47: 128 4.47 - 5.95: 25 5.95 - 7.44: 4 Bond angle restraints: 19098 Sorted by residual: angle pdb=" C PRO A 18 " pdb=" CA PRO A 18 " pdb=" CB PRO A 18 " ideal model delta sigma weight residual 111.64 106.01 5.63 1.27e+00 6.20e-01 1.96e+01 angle pdb=" N PRO A 18 " pdb=" CA PRO A 18 " pdb=" C PRO A 18 " ideal model delta sigma weight residual 111.26 117.97 -6.71 1.63e+00 3.76e-01 1.69e+01 angle pdb=" N HIS B 281 " pdb=" CA HIS B 281 " pdb=" CB HIS B 281 " ideal model delta sigma weight residual 114.17 109.59 4.58 1.14e+00 7.69e-01 1.62e+01 angle pdb=" CA ARG A 49 " pdb=" C ARG A 49 " pdb=" O ARG A 49 " ideal model delta sigma weight residual 122.44 117.24 5.20 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N GLY B 105 " pdb=" CA GLY B 105 " pdb=" C GLY B 105 " ideal model delta sigma weight residual 111.93 116.22 -4.29 1.15e+00 7.56e-01 1.39e+01 ... (remaining 19093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7438 17.96 - 35.93: 719 35.93 - 53.89: 107 53.89 - 71.85: 21 71.85 - 89.82: 18 Dihedral angle restraints: 8303 sinusoidal: 3309 harmonic: 4994 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N GLU A 511 " pdb=" CA GLU A 511 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA CYS B 185 " pdb=" C CYS B 185 " pdb=" N ARG B 186 " pdb=" CA ARG B 186 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP A 513 " pdb=" C ASP A 513 " pdb=" N THR A 514 " pdb=" CA THR A 514 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 8300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1597 0.048 - 0.096: 414 0.096 - 0.144: 121 0.144 - 0.192: 4 0.192 - 0.240: 2 Chirality restraints: 2138 Sorted by residual: chirality pdb=" CA SAM C 602 " pdb=" N SAM C 602 " pdb=" C SAM C 602 " pdb=" CB SAM C 602 " both_signs ideal model delta sigma weight residual False 2.45 2.69 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 15 " pdb=" N ILE A 15 " pdb=" C ILE A 15 " pdb=" CB ILE A 15 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA VAL A 699 " pdb=" N VAL A 699 " pdb=" C VAL A 699 " pdb=" CB VAL A 699 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 2135 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 236 " -0.013 2.00e-02 2.50e+03 1.25e-02 3.92e+00 pdb=" CG TRP B 236 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 236 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 236 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 236 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 236 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 236 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 236 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 369 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO C 370 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 20 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 21 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.021 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 926 2.73 - 3.27: 13490 3.27 - 3.82: 21333 3.82 - 4.36: 25000 4.36 - 4.90: 44063 Nonbonded interactions: 104812 Sorted by model distance: nonbonded pdb=" OE1 GLN C 248 " pdb=" NH1 ARG C 260 " model vdw 2.189 3.120 nonbonded pdb=" OG SER A 118 " pdb=" OD1 ASP A 120 " model vdw 2.199 3.040 nonbonded pdb=" O ARG B 237 " pdb=" OG1 THR B 273 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 609 " pdb=" OD1 ASP A 627 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 132 " model vdw 2.207 3.040 ... (remaining 104807 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.780 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.970 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.003 0.038 14070 Z= 0.186 Angle : 0.699 7.442 19107 Z= 0.413 Chirality : 0.046 0.240 2138 Planarity : 0.004 0.045 2427 Dihedral : 14.666 89.816 5069 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer: Outliers : 0.07 % Allowed : 0.66 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1692 helix: -0.24 (0.39), residues: 180 sheet: -0.67 (0.23), residues: 535 loop : -2.62 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.013 0.001 TYR C 111 PHE 0.018 0.001 PHE A 228 TRP 0.033 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.19 (14067) covalent geometry : angle 0.69789 / 0.41 (19098) hydrogen bonds : bond 0.16343 / 11.16 ( 377) hydrogen bonds : angle 7.31382 / 5.02 ( 1008) metal coordination : bond 0.01315 / 0.66 ( 3) metal coordination : angle 2.17346 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 GLU cc_start: 0.8015 (tp30) cc_final: 0.7715 (tp30) REVERT: C 434 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6460 (mt-10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1116 time to fit residues: 22.5476 Evaluate side-chains 87 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 231 GLN A 659 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 330 GLN B 369 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN C 430 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.107550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089650 restraints weight = 38095.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090882 restraints weight = 39541.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091247 restraints weight = 30814.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092474 restraints weight = 21961.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092459 restraints weight = 17748.626| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14070 Z= 0.106 Angle : 0.563 7.619 19107 Z= 0.295 Chirality : 0.045 0.155 2138 Planarity : 0.004 0.043 2427 Dihedral : 4.942 29.375 1862 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.20), residues: 1692 helix: 0.04 (0.39), residues: 183 sheet: -0.43 (0.23), residues: 535 loop : -2.63 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.015 0.001 TYR A 449 PHE 0.013 0.001 PHE B 684 TRP 0.018 0.001 TRP B 236 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14067) covalent geometry : angle 0.55910 / 0.29 (19098) hydrogen bonds : bond 0.03330 / 2.38 ( 377) hydrogen bonds : angle 5.70858 / 3.86 ( 1008) metal coordination : bond 0.01188 / 0.59 ( 3) metal coordination : angle 3.24471 / 1.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 GLU cc_start: 0.7823 (tp30) cc_final: 0.7517 (tp30) REVERT: C 434 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6841 (mt-10) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1129 time to fit residues: 23.8102 Evaluate side-chains 89 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 229 GLN B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083774 restraints weight = 39787.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083342 restraints weight = 36814.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084096 restraints weight = 33253.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084774 restraints weight = 22600.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085051 restraints weight = 20165.768| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.180 14070 Z= 0.296 Angle : 0.777 13.239 19107 Z= 0.400 Chirality : 0.052 0.241 2138 Planarity : 0.006 0.051 2427 Dihedral : 6.126 31.606 1862 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.94 % Favored : 87.00 % Rotamer: Outliers : 0.13 % Allowed : 8.35 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.19), residues: 1692 helix: -0.81 (0.36), residues: 182 sheet: -0.72 (0.23), residues: 534 loop : -2.96 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 260 TYR 0.018 0.002 TYR C 181 PHE 0.021 0.003 PHE A 604 TRP 0.018 0.002 TRP B 236 HIS 0.012 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.30 (14067) covalent geometry : angle 0.75655 / 0.40 (19098) hydrogen bonds : bond 0.05242 / 3.78 ( 377) hydrogen bonds : angle 6.30389 / 4.29 ( 1008) metal coordination : bond 0.02713 / 1.34 ( 3) metal coordination : angle 8.29000 / 4.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8395 (mmp) cc_final: 0.8147 (mmt) REVERT: B 552 LEU cc_start: 0.8460 (tp) cc_final: 0.8240 (tp) REVERT: C 135 MET cc_start: 0.6974 (pmm) cc_final: 0.6751 (pmm) REVERT: C 347 GLU cc_start: 0.8079 (tp30) cc_final: 0.7731 (tp30) outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.1136 time to fit residues: 18.9972 Evaluate side-chains 76 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN B 229 GLN B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.106959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088489 restraints weight = 38263.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090251 restraints weight = 37725.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090556 restraints weight = 28547.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091926 restraints weight = 21167.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091887 restraints weight = 17582.052| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14070 Z= 0.107 Angle : 0.589 12.499 19107 Z= 0.304 Chirality : 0.047 0.149 2138 Planarity : 0.004 0.047 2427 Dihedral : 5.226 28.883 1862 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.20), residues: 1692 helix: -0.16 (0.39), residues: 183 sheet: -0.50 (0.23), residues: 535 loop : -2.74 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 260 TYR 0.012 0.001 TYR C 181 PHE 0.017 0.001 PHE B 387 TRP 0.016 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14067) covalent geometry : angle 0.57584 / 0.30 (19098) hydrogen bonds : bond 0.03236 / 2.28 ( 377) hydrogen bonds : angle 5.56521 / 3.78 ( 1008) metal coordination : bond 0.01425 / 0.72 ( 3) metal coordination : angle 5.79202 / 3.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8224 (mmp) cc_final: 0.7955 (mmt) REVERT: C 347 GLU cc_start: 0.7879 (tp30) cc_final: 0.7564 (tp30) REVERT: C 382 ASN cc_start: 0.7709 (p0) cc_final: 0.7351 (p0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1205 time to fit residues: 24.2509 Evaluate side-chains 87 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 435 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 593 HIS C 150 HIS ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084982 restraints weight = 39719.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087131 restraints weight = 41830.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087388 restraints weight = 27947.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087469 restraints weight = 21884.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087845 restraints weight = 20570.543| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 14070 Z= 0.250 Angle : 0.722 13.426 19107 Z= 0.370 Chirality : 0.051 0.238 2138 Planarity : 0.005 0.048 2427 Dihedral : 5.906 33.547 1862 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.35 % Favored : 87.59 % Rotamer: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.19), residues: 1692 helix: -0.73 (0.37), residues: 184 sheet: -0.79 (0.23), residues: 538 loop : -2.93 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 260 TYR 0.019 0.002 TYR A 449 PHE 0.016 0.002 PHE A 604 TRP 0.017 0.002 TRP A 509 HIS 0.012 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (14067) covalent geometry : angle 0.70104 / 0.37 (19098) hydrogen bonds : bond 0.04603 / 3.29 ( 377) hydrogen bonds : angle 6.04142 / 4.09 ( 1008) metal coordination : bond 0.02038 / 1.00 ( 3) metal coordination : angle 8.07081 / 4.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8507 (mmp) cc_final: 0.7568 (mmt) REVERT: A 449 TYR cc_start: 0.7439 (t80) cc_final: 0.7111 (t80) REVERT: C 382 ASN cc_start: 0.7546 (p0) cc_final: 0.7217 (p0) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1116 time to fit residues: 18.3406 Evaluate side-chains 79 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 64 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088118 restraints weight = 38848.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089914 restraints weight = 41135.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090670 restraints weight = 27082.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.090839 restraints weight = 21361.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091137 restraints weight = 20797.452| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14070 Z= 0.107 Angle : 0.595 11.797 19107 Z= 0.306 Chirality : 0.046 0.165 2138 Planarity : 0.004 0.044 2427 Dihedral : 5.265 31.397 1862 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1692 helix: -0.39 (0.37), residues: 183 sheet: -0.65 (0.23), residues: 551 loop : -2.71 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 211 TYR 0.011 0.001 TYR C 181 PHE 0.014 0.001 PHE B 684 TRP 0.019 0.001 TRP B 236 HIS 0.004 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14067) covalent geometry : angle 0.58197 / 0.31 (19098) hydrogen bonds : bond 0.03292 / 2.30 ( 377) hydrogen bonds : angle 5.48288 / 3.71 ( 1008) metal coordination : bond 0.01198 / 0.61 ( 3) metal coordination : angle 5.65721 / 3.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 LEU cc_start: 0.8072 (pt) cc_final: 0.7290 (pt) REVERT: C 135 MET cc_start: 0.7034 (pmm) cc_final: 0.6808 (pmm) REVERT: C 347 GLU cc_start: 0.8216 (tp30) cc_final: 0.7815 (tp30) REVERT: C 382 ASN cc_start: 0.7425 (p0) cc_final: 0.7207 (p0) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.1225 time to fit residues: 23.2130 Evaluate side-chains 87 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 9 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 161 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 634 ASN B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN B 590 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.106501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087805 restraints weight = 38520.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089403 restraints weight = 39122.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089743 restraints weight = 30950.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090142 restraints weight = 22517.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090491 restraints weight = 20343.030| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14070 Z= 0.109 Angle : 0.593 11.142 19107 Z= 0.303 Chirality : 0.046 0.156 2138 Planarity : 0.004 0.045 2427 Dihedral : 5.126 31.878 1862 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 0.13 % Allowed : 1.71 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.19), residues: 1692 helix: -0.27 (0.37), residues: 183 sheet: -0.62 (0.22), residues: 561 loop : -2.66 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 260 TYR 0.011 0.001 TYR A 328 PHE 0.013 0.001 PHE B 684 TRP 0.028 0.001 TRP B 236 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14067) covalent geometry : angle 0.58196 / 0.30 (19098) hydrogen bonds : bond 0.03232 / 2.25 ( 377) hydrogen bonds : angle 5.42280 / 3.67 ( 1008) metal coordination : bond 0.01118 / 0.56 ( 3) metal coordination : angle 5.25911 / 3.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 LEU cc_start: 0.7661 (pt) cc_final: 0.7411 (pt) REVERT: C 347 GLU cc_start: 0.8221 (tp30) cc_final: 0.7852 (tp30) REVERT: C 382 ASN cc_start: 0.7668 (p0) cc_final: 0.7393 (p0) outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.1175 time to fit residues: 21.8469 Evaluate side-chains 87 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 124 optimal weight: 7.9990 chunk 165 optimal weight: 0.0030 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN B 590 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086812 restraints weight = 38660.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.089224 restraints weight = 39428.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089265 restraints weight = 28158.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089564 restraints weight = 21123.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089855 restraints weight = 19236.779| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14070 Z= 0.134 Angle : 0.608 10.960 19107 Z= 0.311 Chirality : 0.047 0.170 2138 Planarity : 0.005 0.086 2427 Dihedral : 5.269 32.878 1862 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.93 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.19), residues: 1692 helix: -0.31 (0.38), residues: 183 sheet: -0.68 (0.22), residues: 568 loop : -2.63 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.013 0.001 TYR C 181 PHE 0.013 0.001 PHE A 207 TRP 0.032 0.001 TRP B 236 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14067) covalent geometry : angle 0.59539 / 0.31 (19098) hydrogen bonds : bond 0.03442 / 2.45 ( 377) hydrogen bonds : angle 5.40344 / 3.65 ( 1008) metal coordination : bond 0.01216 / 0.61 ( 3) metal coordination : angle 5.68882 / 3.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7031 (pmm) cc_final: 0.6806 (pmm) REVERT: C 347 GLU cc_start: 0.8205 (tp30) cc_final: 0.7756 (tp30) REVERT: C 382 ASN cc_start: 0.7445 (p0) cc_final: 0.7188 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1049 time to fit residues: 18.9194 Evaluate side-chains 84 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 0.7980 chunk 167 optimal weight: 0.0050 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.106626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088212 restraints weight = 38417.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089774 restraints weight = 41200.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090278 restraints weight = 30186.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090700 restraints weight = 22925.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.090992 restraints weight = 21146.632| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14070 Z= 0.112 Angle : 0.597 10.662 19107 Z= 0.304 Chirality : 0.046 0.164 2138 Planarity : 0.004 0.044 2427 Dihedral : 5.081 32.322 1862 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.20), residues: 1692 helix: -0.17 (0.38), residues: 184 sheet: -0.58 (0.22), residues: 566 loop : -2.59 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 782 TYR 0.019 0.001 TYR B 344 PHE 0.014 0.001 PHE B 685 TRP 0.032 0.001 TRP B 236 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (14067) covalent geometry : angle 0.58670 / 0.30 (19098) hydrogen bonds : bond 0.03220 / 2.25 ( 377) hydrogen bonds : angle 5.25479 / 3.55 ( 1008) metal coordination : bond 0.01155 / 0.58 ( 3) metal coordination : angle 5.08243 / 2.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7030 (pmm) cc_final: 0.6788 (pmm) REVERT: C 323 ILE cc_start: 0.8569 (mt) cc_final: 0.8366 (mm) REVERT: C 347 GLU cc_start: 0.8196 (tp30) cc_final: 0.7781 (tp30) REVERT: C 382 ASN cc_start: 0.7390 (p0) cc_final: 0.7137 (p0) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1147 time to fit residues: 21.4122 Evaluate side-chains 89 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087211 restraints weight = 38412.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089485 restraints weight = 39443.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090017 restraints weight = 24172.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090248 restraints weight = 18967.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090535 restraints weight = 18432.403| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14070 Z= 0.131 Angle : 0.610 10.586 19107 Z= 0.311 Chirality : 0.047 0.157 2138 Planarity : 0.004 0.044 2427 Dihedral : 5.165 33.092 1862 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.63 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.20), residues: 1692 helix: -0.27 (0.37), residues: 183 sheet: -0.56 (0.23), residues: 554 loop : -2.60 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.013 0.001 TYR C 181 PHE 0.013 0.001 PHE B 685 TRP 0.029 0.001 TRP B 236 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14067) covalent geometry : angle 0.59884 / 0.31 (19098) hydrogen bonds : bond 0.03411 / 2.41 ( 377) hydrogen bonds : angle 5.36259 / 3.63 ( 1008) metal coordination : bond 0.01203 / 0.60 ( 3) metal coordination : angle 5.47790 / 3.07 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 GLU cc_start: 0.8169 (tp30) cc_final: 0.7761 (tp30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1100 time to fit residues: 19.1262 Evaluate side-chains 86 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 733 ASN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.105424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.087078 restraints weight = 38900.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088816 restraints weight = 40945.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089750 restraints weight = 27017.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089850 restraints weight = 21396.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090082 restraints weight = 20305.419| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14070 Z= 0.136 Angle : 0.618 11.078 19107 Z= 0.315 Chirality : 0.047 0.163 2138 Planarity : 0.004 0.043 2427 Dihedral : 5.247 32.131 1862 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.20), residues: 1692 helix: -0.31 (0.37), residues: 184 sheet: -0.64 (0.23), residues: 559 loop : -2.62 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 260 TYR 0.014 0.001 TYR B 344 PHE 0.013 0.001 PHE B 685 TRP 0.028 0.001 TRP B 236 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14067) covalent geometry : angle 0.60509 / 0.31 (19098) hydrogen bonds : bond 0.03519 / 2.47 ( 377) hydrogen bonds : angle 5.42595 / 3.67 ( 1008) metal coordination : bond 0.01335 / 0.66 ( 3) metal coordination : angle 5.81568 / 3.23 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.02 seconds wall clock time: 35 minutes 16.30 seconds (2116.30 seconds total)