Starting phenix.real_space_refine on Fri May 16 03:46:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avg_15682/05_2025/8avg_15682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avg_15682/05_2025/8avg_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_15682/05_2025/8avg_15682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avg_15682/05_2025/8avg_15682.map" model { file = "/net/cci-nas-00/data/ceres_data/8avg_15682/05_2025/8avg_15682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avg_15682/05_2025/8avg_15682.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.97, per 1000 atoms: 0.65 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: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.77 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: 5.21 Time building geometry restraints manager: 3.77 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: 7443 17.96 - 35.93: 726 35.93 - 53.89: 115 53.89 - 71.85: 31 71.85 - 89.82: 20 Dihedral angle restraints: 8335 sinusoidal: 3341 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 8332 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: 6.950 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 36.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 15.122 89.816 5101 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.018 0.001 PHE A 228 TYR 0.013 0.001 TYR C 111 ARG 0.004 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.16343 ( 377) hydrogen bonds : angle 7.31382 ( 1008) metal coordination : bond 0.01315 ( 3) metal coordination : angle 2.17346 ( 9) covalent geometry : bond 0.00326 (14067) covalent geometry : angle 0.69789 (19098) *********************** 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 : 1.726 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: 0.2859 time to fit residues: 58.2165 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 : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 0.0980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 659 HIS B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 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 = 0.3769 r_free = 0.3769 target = 0.106219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088130 restraints weight = 38028.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090258 restraints weight = 35568.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.090547 restraints weight = 23584.054| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14070 Z= 0.128 Angle : 0.582 7.657 19107 Z= 0.305 Chirality : 0.046 0.178 2138 Planarity : 0.004 0.045 2427 Dihedral : 7.138 74.495 1894 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1692 helix: -0.06 (0.39), residues: 183 sheet: -0.50 (0.23), residues: 535 loop : -2.68 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 236 HIS 0.010 0.001 HIS C 150 PHE 0.012 0.001 PHE A 207 TYR 0.015 0.001 TYR A 449 ARG 0.006 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 377) hydrogen bonds : angle 5.79371 ( 1008) metal coordination : bond 0.01584 ( 3) metal coordination : angle 3.67809 ( 9) covalent geometry : bond 0.00291 (14067) covalent geometry : angle 0.57616 (19098) *********************** 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 129 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.6913 (pmm) cc_final: 0.6669 (pmm) REVERT: C 347 GLU cc_start: 0.7984 (tp30) cc_final: 0.7668 (tp30) REVERT: C 434 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6835 (mt-10) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2444 time to fit residues: 47.8377 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 : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS ** 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 = 0.3721 r_free = 0.3721 target = 0.103907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085041 restraints weight = 37794.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087444 restraints weight = 35627.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087901 restraints weight = 21060.604| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14070 Z= 0.183 Angle : 0.642 10.869 19107 Z= 0.332 Chirality : 0.048 0.176 2138 Planarity : 0.005 0.044 2427 Dihedral : 7.151 73.801 1894 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.17 % Favored : 88.77 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.19), residues: 1692 helix: -0.32 (0.38), residues: 183 sheet: -0.57 (0.23), residues: 548 loop : -2.78 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.020 0.002 PHE B 387 TYR 0.016 0.002 TYR C 181 ARG 0.008 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 377) hydrogen bonds : angle 5.82421 ( 1008) metal coordination : bond 0.01648 ( 3) metal coordination : angle 6.10828 ( 9) covalent geometry : bond 0.00434 (14067) covalent geometry : angle 0.62814 (19098) *********************** 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 124 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 393 LEU cc_start: 0.8013 (pt) cc_final: 0.7806 (pt) REVERT: B 552 LEU cc_start: 0.8458 (tp) cc_final: 0.8246 (tp) REVERT: C 135 MET cc_start: 0.6895 (pmm) cc_final: 0.6672 (pmm) REVERT: C 347 GLU cc_start: 0.8012 (tp30) cc_final: 0.7679 (tp30) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2392 time to fit residues: 44.7196 Evaluate side-chains 82 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3728 r_free = 0.3728 target = 0.103957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086096 restraints weight = 38406.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087531 restraints weight = 38025.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087863 restraints weight = 28401.774| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14070 Z= 0.191 Angle : 0.658 11.827 19107 Z= 0.339 Chirality : 0.049 0.168 2138 Planarity : 0.005 0.049 2427 Dihedral : 7.006 69.151 1894 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.87 % Favored : 89.07 % Rotamer: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.19), residues: 1692 helix: -0.49 (0.37), residues: 183 sheet: -0.73 (0.23), residues: 553 loop : -2.85 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 433 HIS 0.012 0.001 HIS C 150 PHE 0.013 0.002 PHE A 207 TYR 0.017 0.002 TYR A 449 ARG 0.007 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 377) hydrogen bonds : angle 5.86115 ( 1008) metal coordination : bond 0.01738 ( 3) metal coordination : angle 7.07897 ( 9) covalent geometry : bond 0.00448 (14067) covalent geometry : angle 0.64034 (19098) *********************** 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 119 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7333 (t80) cc_final: 0.6910 (t80) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2350 time to fit residues: 42.7767 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 : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 36 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.8438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS C 430 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087210 restraints weight = 38117.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088782 restraints weight = 35062.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089308 restraints weight = 26377.457| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 0.003 0.076 14070 Z= 0.122 Angle : 0.593 11.387 19107 Z= 0.306 Chirality : 0.047 0.148 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.542 63.876 1894 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1692 helix: -0.26 (0.38), residues: 183 sheet: -0.57 (0.23), residues: 540 loop : -2.74 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.012 0.001 PHE B 684 TYR 0.013 0.001 TYR C 181 ARG 0.005 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 377) hydrogen bonds : angle 5.56846 ( 1008) metal coordination : bond 0.01310 ( 3) metal coordination : angle 5.93675 ( 9) covalent geometry : bond 0.00283 (14067) covalent geometry : angle 0.57876 (19098) *********************** 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 126 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7135 (pmm) cc_final: 0.6808 (pmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2655 time to fit residues: 49.7382 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 : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 0.0030 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN C 150 HIS ** 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 = 0.3758 r_free = 0.3758 target = 0.105668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087599 restraints weight = 38850.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089647 restraints weight = 40410.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090127 restraints weight = 25271.329| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14070 Z= 0.137 Angle : 0.604 11.534 19107 Z= 0.310 Chirality : 0.047 0.149 2138 Planarity : 0.004 0.046 2427 Dihedral : 6.522 63.558 1894 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.81 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1692 helix: -0.20 (0.38), residues: 183 sheet: -0.59 (0.23), residues: 547 loop : -2.72 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 236 HIS 0.008 0.001 HIS B 819 PHE 0.013 0.001 PHE B 612 TYR 0.013 0.001 TYR C 181 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 377) hydrogen bonds : angle 5.50747 ( 1008) metal coordination : bond 0.01374 ( 3) metal coordination : angle 6.25206 ( 9) covalent geometry : bond 0.00318 (14067) covalent geometry : angle 0.58898 (19098) *********************** 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 128 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2437 time to fit residues: 47.3655 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 : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0070 chunk 159 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 606 HIS A 659 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 = 0.3783 r_free = 0.3783 target = 0.107114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089129 restraints weight = 38645.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089540 restraints weight = 40049.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090292 restraints weight = 33714.561| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1760 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= 0.101 Angle : 0.583 11.283 19107 Z= 0.297 Chirality : 0.046 0.142 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.234 58.621 1894 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1692 helix: -0.01 (0.39), residues: 185 sheet: -0.49 (0.23), residues: 540 loop : -2.64 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 236 HIS 0.008 0.001 HIS B 819 PHE 0.015 0.001 PHE B 684 TYR 0.011 0.001 TYR C 181 ARG 0.004 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 377) hydrogen bonds : angle 5.33986 ( 1008) metal coordination : bond 0.01160 ( 3) metal coordination : angle 5.51706 ( 9) covalent geometry : bond 0.00225 (14067) covalent geometry : angle 0.57052 (19098) *********************** 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 128 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 MET cc_start: 0.6676 (ttm) cc_final: 0.6370 (ttm) REVERT: B 820 THR cc_start: 0.7833 (p) cc_final: 0.7615 (p) REVERT: C 382 ASN cc_start: 0.7343 (p0) cc_final: 0.7126 (p0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2492 time to fit residues: 48.2987 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 : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 659 HIS ** B 281 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086850 restraints weight = 38819.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088787 restraints weight = 40388.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089336 restraints weight = 25808.906| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14070 Z= 0.157 Angle : 0.633 12.324 19107 Z= 0.320 Chirality : 0.048 0.184 2138 Planarity : 0.004 0.045 2427 Dihedral : 6.568 64.496 1894 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.70 % Favored : 89.24 % Rotamer: Outliers : 0.07 % Allowed : 1.38 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.19), residues: 1692 helix: -0.18 (0.38), residues: 183 sheet: -0.62 (0.23), residues: 549 loop : -2.65 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 236 HIS 0.009 0.001 HIS B 819 PHE 0.014 0.002 PHE A 207 TYR 0.015 0.001 TYR C 181 ARG 0.006 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 377) hydrogen bonds : angle 5.47551 ( 1008) metal coordination : bond 0.01444 ( 3) metal coordination : angle 7.16895 ( 9) covalent geometry : bond 0.00369 (14067) covalent geometry : angle 0.61413 (19098) *********************** 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 118 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 MET cc_start: 0.6891 (ttm) cc_final: 0.6513 (ttm) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2403 time to fit residues: 43.6110 Evaluate side-chains 78 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 143 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 133 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 281 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.105089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086770 restraints weight = 38546.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088276 restraints weight = 38530.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088719 restraints weight = 28975.350| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14070 Z= 0.150 Angle : 0.637 12.603 19107 Z= 0.321 Chirality : 0.048 0.160 2138 Planarity : 0.004 0.046 2427 Dihedral : 6.567 64.334 1894 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.57 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.19), residues: 1692 helix: -0.29 (0.38), residues: 183 sheet: -0.61 (0.23), residues: 546 loop : -2.68 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 236 HIS 0.007 0.001 HIS B 819 PHE 0.014 0.001 PHE B 685 TYR 0.014 0.001 TYR C 181 ARG 0.005 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 377) hydrogen bonds : angle 5.52500 ( 1008) metal coordination : bond 0.01487 ( 3) metal coordination : angle 7.50238 ( 9) covalent geometry : bond 0.00350 (14067) covalent geometry : angle 0.61552 (19098) *********************** 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 122 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8184 (mmp) cc_final: 0.7665 (mmt) REVERT: A 514 THR cc_start: 0.5697 (m) cc_final: 0.5465 (m) REVERT: B 393 LEU cc_start: 0.8024 (pt) cc_final: 0.7296 (pt) REVERT: B 448 MET cc_start: 0.6850 (ttm) cc_final: 0.6306 (ttm) REVERT: C 347 GLU cc_start: 0.8261 (tp30) cc_final: 0.7871 (tp30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2384 time to fit residues: 44.2110 Evaluate side-chains 81 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.087698 restraints weight = 38538.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088982 restraints weight = 40036.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089368 restraints weight = 32722.007| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14070 Z= 0.129 Angle : 0.622 12.474 19107 Z= 0.314 Chirality : 0.047 0.156 2138 Planarity : 0.004 0.046 2427 Dihedral : 6.438 62.574 1894 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.75 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1692 helix: -0.17 (0.38), residues: 184 sheet: -0.58 (0.23), residues: 551 loop : -2.61 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 236 HIS 0.009 0.001 HIS B 819 PHE 0.014 0.001 PHE B 684 TYR 0.014 0.001 TYR C 181 ARG 0.005 0.000 ARG B 782 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 377) hydrogen bonds : angle 5.47807 ( 1008) metal coordination : bond 0.01386 ( 3) metal coordination : angle 7.05978 ( 9) covalent geometry : bond 0.00300 (14067) covalent geometry : angle 0.60278 (19098) ********************** 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 118 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8263 (mmp) cc_final: 0.7725 (mmt) REVERT: A 115 MET cc_start: 0.7825 (tmm) cc_final: 0.7617 (tmm) REVERT: B 393 LEU cc_start: 0.7572 (pt) cc_final: 0.7267 (pt) REVERT: B 448 MET cc_start: 0.6888 (ttm) cc_final: 0.6213 (ttm) REVERT: B 820 THR cc_start: 0.7866 (p) cc_final: 0.7525 (p) REVERT: C 347 GLU cc_start: 0.8243 (tp30) cc_final: 0.7870 (tp30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2206 time to fit residues: 40.7062 Evaluate side-chains 82 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 78 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 161 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 118 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.088435 restraints weight = 38379.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089439 restraints weight = 38481.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089853 restraints weight = 31619.093| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14070 Z= 0.108 Angle : 0.593 12.059 19107 Z= 0.301 Chirality : 0.046 0.161 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.201 58.732 1894 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.04 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1692 helix: 0.01 (0.39), residues: 184 sheet: -0.45 (0.23), residues: 542 loop : -2.59 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 236 HIS 0.009 0.001 HIS B 819 PHE 0.014 0.001 PHE B 684 TYR 0.013 0.001 TYR C 181 ARG 0.005 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 377) hydrogen bonds : angle 5.29846 ( 1008) metal coordination : bond 0.01208 ( 3) metal coordination : angle 6.33307 ( 9) covalent geometry : bond 0.00243 (14067) covalent geometry : angle 0.57699 (19098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3554.24 seconds wall clock time: 63 minutes 59.45 seconds (3839.45 seconds total)