Starting phenix.real_space_refine on Mon Dec 30 20:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avg_15682/12_2024/8avg_15682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avg_15682/12_2024/8avg_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_15682/12_2024/8avg_15682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avg_15682/12_2024/8avg_15682.map" model { file = "/net/cci-nas-00/data/ceres_data/8avg_15682/12_2024/8avg_15682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avg_15682/12_2024/8avg_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.29, per 1000 atoms: 0.68 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 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: 1.90 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: 4.82 Time building geometry restraints manager: 3.69 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: 3.260 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.920 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.750 ------------------------------------------------------------------------------- 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 14067 Z= 0.215 Angle : 0.698 7.442 19098 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 *********************** 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 : 1.656 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: 0.2440 time to fit residues: 49.0890 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 : 1.707 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 14067 Z= 0.190 Angle : 0.576 7.657 19098 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 *********************** 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 : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7020 (pmm) cc_final: 0.6731 (pmm) REVERT: C 347 GLU cc_start: 0.8092 (tp30) cc_final: 0.7750 (tp30) REVERT: C 434 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6839 (mt-10) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2627 time to fit residues: 51.4731 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 : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 0.0270 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- 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** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14067 Z= 0.192 Angle : 0.573 8.060 19098 Z= 0.302 Chirality : 0.046 0.155 2138 Planarity : 0.004 0.043 2427 Dihedral : 6.766 70.093 1894 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -2.35 (0.20), residues: 1692 helix: -0.04 (0.39), residues: 183 sheet: -0.46 (0.23), residues: 543 loop : -2.67 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.015 0.001 PHE A 515 TYR 0.013 0.001 TYR C 181 ARG 0.006 0.000 ARG C 260 *********************** 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 134 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.6897 (pmm) cc_final: 0.6644 (pmm) REVERT: C 347 GLU cc_start: 0.8081 (tp30) cc_final: 0.7722 (tp30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2628 time to fit residues: 53.3483 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 : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 606 HIS 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** B 593 HIS ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 14067 Z= 0.251 Angle : 0.606 8.382 19098 Z= 0.320 Chirality : 0.047 0.155 2138 Planarity : 0.005 0.050 2427 Dihedral : 6.733 67.909 1894 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.58 % Favored : 89.36 % Rotamer: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.07 % 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: -2.49 (0.20), residues: 1692 helix: -0.25 (0.38), residues: 182 sheet: -0.56 (0.23), residues: 547 loop : -2.74 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 509 HIS 0.012 0.001 HIS C 150 PHE 0.013 0.002 PHE A 207 TYR 0.015 0.001 TYR C 181 ARG 0.007 0.000 ARG C 260 *********************** 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 : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7030 (pmm) cc_final: 0.6733 (pmm) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2560 time to fit residues: 47.0936 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 : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 149 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 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** C 380 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14067 Z= 0.187 Angle : 0.569 7.337 19098 Z= 0.301 Chirality : 0.046 0.152 2138 Planarity : 0.004 0.043 2427 Dihedral : 6.471 63.946 1894 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % 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: -2.37 (0.20), residues: 1692 helix: -0.09 (0.39), residues: 182 sheet: -0.47 (0.23), residues: 539 loop : -2.67 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.012 0.001 PHE A 207 TYR 0.013 0.001 TYR C 181 ARG 0.005 0.000 ARG C 260 *********************** 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 127 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 820 THR cc_start: 0.7939 (p) cc_final: 0.7730 (p) REVERT: C 135 MET cc_start: 0.7029 (pmm) cc_final: 0.6790 (pmm) REVERT: C 382 ASN cc_start: 0.7318 (p0) cc_final: 0.7103 (p0) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2451 time to fit residues: 47.7813 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 : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 166 optimal weight: 0.0470 chunk 138 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 606 HIS 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 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14067 Z= 0.192 Angle : 0.573 6.283 19098 Z= 0.302 Chirality : 0.047 0.145 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.384 62.240 1894 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.87 % Favored : 90.07 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % 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: -2.37 (0.20), residues: 1692 helix: -0.08 (0.39), residues: 182 sheet: -0.54 (0.23), residues: 554 loop : -2.64 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.012 0.001 PHE A 207 TYR 0.013 0.001 TYR C 181 ARG 0.005 0.000 ARG C 260 *********************** 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 127 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2499 time to fit residues: 48.3829 Evaluate side-chains 83 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 121 optimal weight: 0.0970 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14067 Z= 0.184 Angle : 0.580 9.124 19098 Z= 0.302 Chirality : 0.046 0.147 2138 Planarity : 0.004 0.043 2427 Dihedral : 6.317 61.105 1894 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -0.05 (0.39), residues: 182 sheet: -0.53 (0.23), residues: 553 loop : -2.62 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 236 HIS 0.013 0.001 HIS C 150 PHE 0.012 0.001 PHE A 207 TYR 0.013 0.001 TYR C 181 ARG 0.005 0.000 ARG C 260 *********************** 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 126 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.750 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: 0.7056 (pmm) cc_final: 0.6798 (pmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2642 time to fit residues: 51.0071 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 : 1.606 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 0.0050 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 overall best weight: 0.7134 ------------------------------------------------------------------------------- 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 606 HIS 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 150 HIS ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14067 Z= 0.168 Angle : 0.572 8.823 19098 Z= 0.297 Chirality : 0.046 0.181 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.208 58.673 1894 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 0.07 % Allowed : 1.18 % Favored : 98.75 % 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 (0.38), residues: 183 sheet: -0.48 (0.23), residues: 553 loop : -2.58 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.012 0.001 PHE B 684 TYR 0.012 0.001 TYR C 181 ARG 0.004 0.000 ARG C 260 *********************** 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 131 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.630 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: 0.8124 (mmp) cc_final: 0.7503 (mmt) REVERT: A 115 MET cc_start: 0.7837 (tmm) cc_final: 0.7572 (tmm) REVERT: C 135 MET cc_start: 0.7158 (pmm) cc_final: 0.6891 (pmm) REVERT: C 323 ILE cc_start: 0.8654 (mt) cc_final: 0.8401 (mm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2800 time to fit residues: 55.3244 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 : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0570 chunk 158 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14067 Z= 0.210 Angle : 0.597 8.579 19098 Z= 0.310 Chirality : 0.047 0.189 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.389 61.511 1894 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.87 % Favored : 90.07 % 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 (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: -0.36 (0.37), residues: 189 sheet: -0.52 (0.23), residues: 555 loop : -2.62 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.013 0.001 HIS C 150 PHE 0.014 0.001 PHE B 685 TYR 0.019 0.001 TYR A 449 ARG 0.005 0.000 ARG C 260 *********************** 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 119 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8268 (mmp) cc_final: 0.7552 (mmt) REVERT: A 115 MET cc_start: 0.7840 (tmm) cc_final: 0.7581 (tmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2340 time to fit residues: 43.9194 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 : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 0.0040 chunk 113 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 0.0050 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.0020 chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- 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 530 HIS A 545 GLN A 659 HIS B 118 GLN B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN C 147 GLN C 150 HIS ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14067 Z= 0.136 Angle : 0.560 9.905 19098 Z= 0.291 Chirality : 0.046 0.167 2138 Planarity : 0.004 0.043 2427 Dihedral : 5.841 49.787 1894 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % 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 (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: -2.13 (0.20), residues: 1692 helix: -0.04 (0.38), residues: 190 sheet: -0.26 (0.23), residues: 547 loop : -2.54 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.015 0.001 PHE B 684 TYR 0.021 0.001 TYR A 449 ARG 0.003 0.000 ARG C 473 ********************** 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 133 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.894 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: 0.8159 (mmp) cc_final: 0.7568 (mmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2524 time to fit residues: 51.8371 Evaluate side-chains 91 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 733 ASN C 150 HIS ** 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 = 0.3757 r_free = 0.3757 target = 0.105474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087093 restraints weight = 38125.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088645 restraints weight = 37911.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088964 restraints weight = 27890.816| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14067 Z= 0.237 Angle : 0.614 9.522 19098 Z= 0.318 Chirality : 0.048 0.175 2138 Planarity : 0.004 0.043 2427 Dihedral : 6.356 62.474 1894 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.52 % Favored : 90.43 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % 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: -2.21 (0.20), residues: 1692 helix: -0.06 (0.38), residues: 184 sheet: -0.44 (0.23), residues: 556 loop : -2.52 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 236 HIS 0.011 0.001 HIS C 150 PHE 0.014 0.002 PHE A 207 TYR 0.015 0.001 TYR C 181 ARG 0.006 0.000 ARG C 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.43 seconds wall clock time: 47 minutes 38.94 seconds (2858.94 seconds total)