Starting phenix.real_space_refine on Fri Jun 5 19:09:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.cif Found real_map, /net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.map" model { file = "/net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9osi_70807/06_2026/9osi_70807.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 14498 2.51 5 N 3779 2.21 5 O 4222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5589 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 715} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 16, 'PHE:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 13, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 5716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5716 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 727} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 2, 'ASP:plan': 11, 'TYR:plan': 2, 'GLU:plan': 8, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "C" Number of atoms: 5592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5592 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 715} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 16, 'PHE:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 13, 'HIS:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 224 Chain: "D" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5704 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 727} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 353 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 2, 'ASP:plan': 11, 'TYR:plan': 2, 'GLU:plan': 8, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 176 Time building chain proxies: 4.75, per 1000 atoms: 0.21 Number of scatterers: 22601 At special positions: 0 Unit cell: (102.885, 166.782, 203.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4222 8.00 N 3779 7.00 C 14498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 170 " distance=2.02 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 334 " distance=2.03 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 33 sheets defined 45.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.674A pdb=" N GLN A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.684A pdb=" N SER A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 3.664A pdb=" N VAL A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.567A pdb=" N LEU A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.673A pdb=" N ARG A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.758A pdb=" N VAL A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 484 through 490 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 543 through 564 removed outlier: 4.046A pdb=" N TRP A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 548 " --> pdb=" O PRO A 544 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 648 removed outlier: 3.575A pdb=" N ILE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 683 through 696 removed outlier: 5.163A pdb=" N MET A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 700 removed outlier: 3.914A pdb=" N VAL A 700 " --> pdb=" O GLN A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 700' Processing helix chain 'A' and resid 704 through 715 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 773 through 783 removed outlier: 3.692A pdb=" N ILE A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 829 removed outlier: 4.076A pdb=" N ILE A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.562A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.547A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.231A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.639A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.674A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 4.129A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.681A pdb=" N ARG B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.682A pdb=" N LYS B 525 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 526 " --> pdb=" O ARG B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 526' Processing helix chain 'B' and resid 560 through 583 Processing helix chain 'B' and resid 631 through 661 Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.786A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.692A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 747 Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.737A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 820 through 844 removed outlier: 4.002A pdb=" N PHE B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.923A pdb=" N SER C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 219 through 232 Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.649A pdb=" N LEU C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 325 removed outlier: 3.768A pdb=" N VAL C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 438 through 441 Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.654A pdb=" N GLU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 490 Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 543 through 565 removed outlier: 3.803A pdb=" N TRP C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 648 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 672 through 679 Processing helix chain 'C' and resid 683 through 696 removed outlier: 3.599A pdb=" N LYS C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 700 removed outlier: 3.542A pdb=" N VAL C 700 " --> pdb=" O GLN C 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 697 through 700' Processing helix chain 'C' and resid 704 through 715 removed outlier: 4.061A pdb=" N LEU C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.773A pdb=" N TYR C 728 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS C 729 " --> pdb=" O MET C 725 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 731 " --> pdb=" O GLU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 773 Processing helix chain 'C' and resid 773 through 783 removed outlier: 3.837A pdb=" N ILE C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 829 removed outlier: 3.831A pdb=" N PHE C 808 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 810 " --> pdb=" O GLY C 806 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 829 " --> pdb=" O GLU C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 4.083A pdb=" N ILE D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 removed outlier: 3.613A pdb=" N CYS D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.831A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.083A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.573A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 297 removed outlier: 3.722A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.596A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 4.107A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.622A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.808A pdb=" N ARG D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 561 through 583 removed outlier: 4.043A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D 566 " --> pdb=" O ASP D 562 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 582 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 661 removed outlier: 4.379A pdb=" N THR D 652 " --> pdb=" O ILE D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 677 removed outlier: 4.157A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.799A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.540A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.661A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 747 through 749 No H-bonds generated for 'chain 'D' and resid 747 through 749' Processing helix chain 'D' and resid 773 through 788 removed outlier: 4.145A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.584A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 845 removed outlier: 3.542A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 5.808A pdb=" N LEU A 24 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP A 66 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET A 26 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 68 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA A 28 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N SER A 92 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG A 25 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LEU A 94 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 27 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.749A pdb=" N SER A 189 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 162 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP A 217 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 164 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N PHE A 267 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LEU A 244 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 266 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 389 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.804A pdb=" N GLU A 363 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 466 removed outlier: 6.573A pdb=" N VAL A 419 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 497 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA A 498 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY A 749 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA6, first strand: chain 'A' and resid 665 through 666 removed outlier: 6.334A pdb=" N GLU A 665 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU A 720 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N TYR A 717 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG A 526 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 719 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 43 removed outlier: 7.127A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.331A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.310A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.582A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.613A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 398 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 478 through 482 removed outlier: 3.546A pdb=" N VAL B 514 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 513 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 767 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA B 515 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY B 765 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 517 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B 763 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 478 through 482 removed outlier: 3.546A pdb=" N VAL B 514 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 513 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 767 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA B 515 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY B 765 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 517 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B 763 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB6, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB7, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.377A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 542 " --> pdb=" O THR B 753 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 63 through 69 removed outlier: 5.824A pdb=" N LEU C 24 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP C 66 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET C 26 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 68 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 28 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ARG C 25 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N LEU C 94 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 27 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 93 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.736A pdb=" N SER C 189 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER C 162 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP C 217 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 164 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR C 242 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N PHE C 267 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LEU C 244 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE C 264 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 389 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU C 379 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU C 387 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.506A pdb=" N TYR C 355 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 464 through 466 removed outlier: 6.440A pdb=" N VAL C 419 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR C 420 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA C 499 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA C 498 " --> pdb=" O GLY C 749 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY C 749 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 500 " --> pdb=" O GLY C 747 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY C 747 " --> pdb=" O PHE C 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 464 through 466 removed outlier: 6.440A pdb=" N VAL C 419 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR C 420 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA C 499 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA C 498 " --> pdb=" O GLY C 749 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY C 749 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 500 " --> pdb=" O GLY C 747 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY C 747 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 517 " --> pdb=" O TYR C 748 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AC5, first strand: chain 'C' and resid 719 through 722 Processing sheet with id=AC6, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.528A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 40 through 43 removed outlier: 6.470A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.433A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.781A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 171 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE D 227 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 392 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 398 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.583A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 478 through 482 removed outlier: 3.633A pdb=" N THR D 437 " --> pdb=" O ARG D 481 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE D 434 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD4, first strand: chain 'D' and resid 517 through 518 removed outlier: 3.993A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD6, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.757A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 539 " --> pdb=" O MET D 737 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2808 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: 3.91 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3710 1.28 - 1.41: 5743 1.41 - 1.55: 13412 1.55 - 1.68: 20 1.68 - 1.82: 174 Bond restraints: 23059 Sorted by residual: bond pdb=" CA THR A 636 " pdb=" C THR A 636 " ideal model delta sigma weight residual 1.522 1.401 0.121 1.39e-02 5.18e+03 7.56e+01 bond pdb=" CA SER A 633 " pdb=" C SER A 633 " ideal model delta sigma weight residual 1.522 1.408 0.114 1.39e-02 5.18e+03 6.71e+01 bond pdb=" CA SER A 634 " pdb=" C SER A 634 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.27e-02 6.20e+03 5.45e+01 bond pdb=" C THR A 636 " pdb=" O THR A 636 " ideal model delta sigma weight residual 1.236 1.147 0.090 1.24e-02 6.50e+03 5.22e+01 bond pdb=" CA LEU B 655 " pdb=" C LEU B 655 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.29e-02 6.01e+03 5.19e+01 ... (remaining 23054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 30800 3.28 - 6.55: 511 6.55 - 9.83: 73 9.83 - 13.10: 8 13.10 - 16.38: 4 Bond angle restraints: 31396 Sorted by residual: angle pdb=" N ASN B 819 " pdb=" CA ASN B 819 " pdb=" C ASN B 819 " ideal model delta sigma weight residual 113.88 97.50 16.38 1.23e+00 6.61e-01 1.77e+02 angle pdb=" N ILE D 563 " pdb=" CA ILE D 563 " pdb=" C ILE D 563 " ideal model delta sigma weight residual 110.62 120.30 -9.68 1.02e+00 9.61e-01 9.01e+01 angle pdb=" N GLU D 811 " pdb=" CA GLU D 811 " pdb=" C GLU D 811 " ideal model delta sigma weight residual 108.41 123.80 -15.39 1.63e+00 3.76e-01 8.92e+01 angle pdb=" N ILE B 563 " pdb=" CA ILE B 563 " pdb=" C ILE B 563 " ideal model delta sigma weight residual 111.05 100.96 10.09 1.25e+00 6.40e-01 6.52e+01 angle pdb=" N ASP D 562 " pdb=" CA ASP D 562 " pdb=" C ASP D 562 " ideal model delta sigma weight residual 111.36 102.76 8.60 1.09e+00 8.42e-01 6.23e+01 ... (remaining 31391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12278 17.97 - 35.93: 1170 35.93 - 53.90: 192 53.90 - 71.86: 29 71.86 - 89.83: 13 Dihedral angle restraints: 13682 sinusoidal: 4968 harmonic: 8714 Sorted by residual: dihedral pdb=" C ASN B 819 " pdb=" N ASN B 819 " pdb=" CA ASN B 819 " pdb=" CB ASN B 819 " ideal model delta harmonic sigma weight residual -122.60 -103.85 -18.75 0 2.50e+00 1.60e-01 5.62e+01 dihedral pdb=" CB CYS C 36 " pdb=" SG CYS C 36 " pdb=" SG CYS C 292 " pdb=" CB CYS C 292 " ideal model delta sinusoidal sigma weight residual 93.00 28.93 64.07 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CA LEU C 732 " pdb=" C LEU C 732 " pdb=" N ASN C 733 " pdb=" CA ASN C 733 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 13679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3535 0.124 - 0.248: 148 0.248 - 0.373: 8 0.373 - 0.497: 6 0.497 - 0.621: 2 Chirality restraints: 3699 Sorted by residual: chirality pdb=" CA ASN B 654 " pdb=" N ASN B 654 " pdb=" C ASN B 654 " pdb=" CB ASN B 654 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CA ILE D 648 " pdb=" N ILE D 648 " pdb=" C ILE D 648 " pdb=" CB ILE D 648 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CA LEU C 643 " pdb=" N LEU C 643 " pdb=" C LEU C 643 " pdb=" CB LEU C 643 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 3696 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 562 " -0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C ASP B 562 " 0.101 2.00e-02 2.50e+03 pdb=" O ASP B 562 " -0.039 2.00e-02 2.50e+03 pdb=" N ILE B 563 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 531 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ARG A 531 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 531 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A 532 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 699 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER C 699 " -0.064 2.00e-02 2.50e+03 pdb=" O SER C 699 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL C 700 " 0.022 2.00e-02 2.50e+03 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 54 2.32 - 2.97: 10569 2.97 - 3.61: 33002 3.61 - 4.26: 50297 4.26 - 4.90: 82146 Nonbonded interactions: 176068 Sorted by model distance: nonbonded pdb=" N HIS C 670 " pdb=" O VAL C 702 " model vdw 1.675 3.120 nonbonded pdb=" CE2 PHE D 555 " pdb=" CD1 ILE D 823 " model vdw 1.701 3.760 nonbonded pdb=" N GLY B 816 " pdb=" OD1 ASN B 819 " model vdw 1.868 3.120 nonbonded pdb=" O THR C 668 " pdb=" CB VAL C 702 " model vdw 1.928 3.470 nonbonded pdb=" CG2 ILE B 563 " pdb=" CD1 ILE C 804 " model vdw 2.005 3.880 ... (remaining 176063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 21 through 539 or (resid 540 and (name N or name CA or nam \ e C or name O or name CB )) or resid 541 through 829)) } ncs_group { reference = (chain 'B' and (resid 33 through 562 or (resid 563 through 565 and (name N or na \ me CA or name C or name O or name CB )) or resid 566 through 845)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.930 Find NCS groups from input model: 0.530 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 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 : 0.009 0.297 23068 Z= 0.502 Angle : 1.094 16.378 31412 Z= 0.660 Chirality : 0.063 0.621 3699 Planarity : 0.007 0.081 3988 Dihedral : 14.372 89.830 8042 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.14 % Favored : 93.76 % Rotamer: Outliers : 1.00 % Allowed : 10.44 % Favored : 88.57 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.12), residues: 2980 helix: -2.71 (0.10), residues: 1280 sheet: -2.64 (0.22), residues: 391 loop : -3.00 (0.14), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 647 TYR 0.036 0.002 TYR C 554 PHE 0.034 0.003 PHE C 542 TRP 0.033 0.003 TRP C 625 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.46 (23059) covalent geometry : angle 1.09384 / 0.66 (31396) SS BOND : bond 0.00320 / 0.16 ( 8) SS BOND : angle 0.86296 / 0.44 ( 16) hydrogen bonds : bond 0.18155 / 12.54 ( 958) hydrogen bonds : angle 7.85156 / 5.43 ( 2808) Misc. bond : bond 0.29724 / 15.64 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 376 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: B 234 MET cc_start: 0.8801 (tpp) cc_final: 0.8565 (tpp) REVERT: B 248 MET cc_start: 0.8480 (mmm) cc_final: 0.8126 (mmm) REVERT: B 360 MET cc_start: 0.7836 (tpt) cc_final: 0.6892 (tpp) REVERT: C 542 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6177 (m-10) REVERT: D 248 MET cc_start: 0.7888 (mmm) cc_final: 0.7546 (mmm) outliers start: 23 outliers final: 5 residues processed: 397 average time/residue: 0.1541 time to fit residues: 95.1002 Evaluate side-chains 203 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0170 chunk 111 optimal weight: 3.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 726 ASN B 73 ASN B 81 GLN B 129 HIS B 288 GLN C 322 ASN C 385 HIS C 490 ASN ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 ASN D 73 ASN D 81 GLN D 119 GLN D 129 HIS D 131 GLN D 196 ASN D 677 GLN ** D 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.140436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.106869 restraints weight = 64850.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102553 restraints weight = 48026.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104163 restraints weight = 44579.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104384 restraints weight = 34685.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.104510 restraints weight = 32603.445| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23068 Z= 0.162 Angle : 0.637 9.706 31412 Z= 0.330 Chirality : 0.042 0.171 3699 Planarity : 0.005 0.049 3988 Dihedral : 5.449 58.633 3236 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.43 % Allowed : 15.11 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 2980 helix: -0.75 (0.13), residues: 1297 sheet: -2.09 (0.24), residues: 420 loop : -2.55 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 634 TYR 0.021 0.001 TYR B 682 PHE 0.041 0.002 PHE B 658 TRP 0.018 0.002 TRP B 799 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (23059) covalent geometry : angle 0.63628 / 0.33 (31396) SS BOND : bond 0.00756 / 0.26 ( 8) SS BOND : angle 1.44412 / 0.83 ( 16) hydrogen bonds : bond 0.04097 / 2.80 ( 958) hydrogen bonds : angle 5.09553 / 3.53 ( 2808) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 811 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8851 (tp) REVERT: B 234 MET cc_start: 0.8866 (tpp) cc_final: 0.8367 (tpp) REVERT: B 360 MET cc_start: 0.8266 (tpt) cc_final: 0.7490 (tpp) REVERT: B 693 PHE cc_start: 0.7712 (m-80) cc_final: 0.7359 (m-80) REVERT: B 799 TRP cc_start: 0.7280 (m-10) cc_final: 0.6862 (m100) REVERT: C 94 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8875 (pp) REVERT: C 204 LYS cc_start: 0.8731 (mttt) cc_final: 0.8259 (tttm) REVERT: C 542 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6847 (m-10) REVERT: C 561 LEU cc_start: 0.8336 (mm) cc_final: 0.8101 (mm) REVERT: D 309 SER cc_start: 0.8492 (p) cc_final: 0.7826 (m) REVERT: D 784 GLN cc_start: 0.8687 (mt0) cc_final: 0.8398 (pp30) outliers start: 56 outliers final: 25 residues processed: 264 average time/residue: 0.1378 time to fit residues: 59.3615 Evaluate side-chains 219 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 170 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 152 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 chunk 274 optimal weight: 0.1980 chunk 189 optimal weight: 9.9990 chunk 292 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN B 792 HIS C 661 GLN D 119 GLN D 131 GLN D 654 ASN ** D 726 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.139117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.104665 restraints weight = 64709.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100569 restraints weight = 47185.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.102258 restraints weight = 43786.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.102449 restraints weight = 35692.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.102471 restraints weight = 31876.954| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23068 Z= 0.137 Angle : 0.584 12.346 31412 Z= 0.296 Chirality : 0.041 0.159 3699 Planarity : 0.004 0.061 3988 Dihedral : 4.675 37.228 3229 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.82 % Allowed : 16.80 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 2980 helix: 0.24 (0.14), residues: 1290 sheet: -1.95 (0.24), residues: 437 loop : -2.19 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 58 TYR 0.017 0.001 TYR B 566 PHE 0.015 0.001 PHE A 820 TRP 0.027 0.002 TRP D 641 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (23059) covalent geometry : angle 0.58320 / 0.30 (31396) SS BOND : bond 0.00264 / 0.12 ( 8) SS BOND : angle 1.06154 / 0.59 ( 16) hydrogen bonds : bond 0.03427 / 2.32 ( 958) hydrogen bonds : angle 4.56700 / 3.18 ( 2808) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 MET cc_start: 0.8739 (tpp) cc_final: 0.8482 (tpp) REVERT: B 248 MET cc_start: 0.8274 (mmm) cc_final: 0.7995 (mmm) REVERT: B 301 LEU cc_start: 0.6601 (mt) cc_final: 0.6309 (mp) REVERT: B 793 MET cc_start: 0.8521 (mtm) cc_final: 0.8311 (ptp) REVERT: C 94 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8813 (pp) REVERT: C 204 LYS cc_start: 0.8746 (mttt) cc_final: 0.8346 (tttp) REVERT: C 542 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: C 561 LEU cc_start: 0.8325 (mm) cc_final: 0.8117 (mm) REVERT: C 661 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: D 309 SER cc_start: 0.8461 (p) cc_final: 0.7903 (m) REVERT: D 413 MET cc_start: 0.8777 (mtp) cc_final: 0.8575 (mtp) REVERT: D 737 MET cc_start: 0.6370 (ttp) cc_final: 0.5759 (ttp) REVERT: D 784 GLN cc_start: 0.8628 (mt0) cc_final: 0.8373 (pp30) REVERT: D 785 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5555 (tp) outliers start: 65 outliers final: 35 residues processed: 259 average time/residue: 0.1300 time to fit residues: 55.8090 Evaluate side-chains 219 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 270 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 238 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 268 optimal weight: 30.0000 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN D 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.108608 restraints weight = 64914.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106417 restraints weight = 58023.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107610 restraints weight = 55324.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107658 restraints weight = 39814.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107767 restraints weight = 36069.493| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23068 Z= 0.111 Angle : 0.563 13.800 31412 Z= 0.280 Chirality : 0.040 0.149 3699 Planarity : 0.003 0.058 3988 Dihedral : 4.386 35.205 3228 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.34 % Allowed : 17.89 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 2980 helix: 0.70 (0.15), residues: 1299 sheet: -1.86 (0.24), residues: 418 loop : -2.02 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 351 TYR 0.018 0.001 TYR B 566 PHE 0.018 0.001 PHE B 643 TRP 0.046 0.001 TRP C 783 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (23059) covalent geometry : angle 0.56251 / 0.28 (31396) SS BOND : bond 0.00231 / 0.10 ( 8) SS BOND : angle 0.94594 / 0.49 ( 16) hydrogen bonds : bond 0.03047 / 2.05 ( 958) hydrogen bonds : angle 4.30230 / 3.00 ( 2808) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.7418 (mt) cc_final: 0.7110 (mt) REVERT: A 643 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 234 MET cc_start: 0.8699 (tpp) cc_final: 0.8437 (tpp) REVERT: B 248 MET cc_start: 0.8426 (mmm) cc_final: 0.8156 (mmm) REVERT: B 445 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6378 (pp) REVERT: C 82 MET cc_start: 0.7153 (tmm) cc_final: 0.6878 (tmm) REVERT: C 94 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8693 (pp) REVERT: C 204 LYS cc_start: 0.8703 (mttt) cc_final: 0.8358 (tttp) REVERT: C 542 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6161 (m-10) REVERT: C 547 TRP cc_start: 0.6459 (m100) cc_final: 0.5144 (m100) REVERT: C 675 MET cc_start: 0.7607 (tpt) cc_final: 0.7285 (tpp) REVERT: D 309 SER cc_start: 0.8397 (p) cc_final: 0.7899 (m) REVERT: D 413 MET cc_start: 0.8775 (mtp) cc_final: 0.8534 (mtp) REVERT: D 785 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5181 (tp) outliers start: 54 outliers final: 27 residues processed: 234 average time/residue: 0.1283 time to fit residues: 50.5072 Evaluate side-chains 209 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 64 optimal weight: 20.0000 chunk 30 optimal weight: 0.1980 chunk 135 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 157 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 281 optimal weight: 30.0000 chunk 39 optimal weight: 0.0060 chunk 191 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 overall best weight: 0.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.138871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105596 restraints weight = 64274.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101514 restraints weight = 57822.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.102695 restraints weight = 48537.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104063 restraints weight = 38834.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.103754 restraints weight = 33483.908| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23068 Z= 0.118 Angle : 0.563 15.734 31412 Z= 0.278 Chirality : 0.040 0.144 3699 Planarity : 0.003 0.054 3988 Dihedral : 4.195 32.495 3226 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.90 % Allowed : 18.19 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2980 helix: 1.01 (0.15), residues: 1294 sheet: -1.84 (0.24), residues: 429 loop : -1.83 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 351 TYR 0.022 0.001 TYR C 554 PHE 0.020 0.001 PHE B 643 TRP 0.035 0.001 TRP B 799 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23059) covalent geometry : angle 0.56305 / 0.28 (31396) SS BOND : bond 0.00227 / 0.10 ( 8) SS BOND : angle 0.90999 / 0.47 ( 16) hydrogen bonds : bond 0.02910 / 1.97 ( 958) hydrogen bonds : angle 4.21154 / 2.94 ( 2808) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.7300 (mt) cc_final: 0.6947 (mt) REVERT: A 643 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8289 (mp) REVERT: B 234 MET cc_start: 0.8718 (tpp) cc_final: 0.8486 (tpp) REVERT: B 248 MET cc_start: 0.8397 (mmm) cc_final: 0.8123 (mmm) REVERT: B 445 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6924 (pp) REVERT: B 799 TRP cc_start: 0.7216 (m100) cc_final: 0.6983 (m100) REVERT: C 51 ILE cc_start: 0.7751 (mt) cc_final: 0.7518 (tp) REVERT: C 82 MET cc_start: 0.7153 (tmm) cc_final: 0.6930 (tmm) REVERT: C 94 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8776 (pp) REVERT: C 204 LYS cc_start: 0.8668 (mttt) cc_final: 0.8345 (tttp) REVERT: C 340 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.6923 (t60) REVERT: C 542 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6062 (m-10) REVERT: C 547 TRP cc_start: 0.6556 (m100) cc_final: 0.5122 (m100) REVERT: C 550 MET cc_start: 0.5467 (ttt) cc_final: 0.5230 (ttt) REVERT: C 561 LEU cc_start: 0.8099 (mm) cc_final: 0.7811 (mm) REVERT: C 675 MET cc_start: 0.8167 (tpt) cc_final: 0.7803 (tpp) REVERT: D 309 SER cc_start: 0.8320 (p) cc_final: 0.7838 (m) outliers start: 67 outliers final: 35 residues processed: 244 average time/residue: 0.1223 time to fit residues: 50.3756 Evaluate side-chains 221 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 202 optimal weight: 10.0000 chunk 101 optimal weight: 0.0060 chunk 264 optimal weight: 0.1980 chunk 271 optimal weight: 7.9990 chunk 187 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 63 optimal weight: 20.0000 chunk 292 optimal weight: 20.0000 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.138418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106000 restraints weight = 64690.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100675 restraints weight = 53755.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102019 restraints weight = 56090.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102389 restraints weight = 44280.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.102554 restraints weight = 39916.866| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23068 Z= 0.114 Angle : 0.556 16.026 31412 Z= 0.273 Chirality : 0.040 0.172 3699 Planarity : 0.003 0.053 3988 Dihedral : 4.079 32.424 3226 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.69 % Allowed : 18.36 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2980 helix: 1.20 (0.15), residues: 1297 sheet: -1.81 (0.24), residues: 431 loop : -1.72 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 351 TYR 0.020 0.001 TYR C 554 PHE 0.020 0.001 PHE B 643 TRP 0.021 0.001 TRP D 641 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (23059) covalent geometry : angle 0.55625 / 0.27 (31396) SS BOND : bond 0.00244 / 0.11 ( 8) SS BOND : angle 0.88051 / 0.45 ( 16) hydrogen bonds : bond 0.02848 / 1.93 ( 958) hydrogen bonds : angle 4.13380 / 2.89 ( 2808) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.7217 (mt) cc_final: 0.6999 (mt) REVERT: B 234 MET cc_start: 0.8460 (tpp) cc_final: 0.8156 (tpp) REVERT: B 248 MET cc_start: 0.8332 (mmm) cc_final: 0.7997 (mmm) REVERT: B 799 TRP cc_start: 0.7418 (m100) cc_final: 0.7078 (m100) REVERT: C 51 ILE cc_start: 0.7780 (mt) cc_final: 0.7565 (tp) REVERT: C 82 MET cc_start: 0.7216 (tmm) cc_final: 0.6991 (tmm) REVERT: C 94 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 204 LYS cc_start: 0.8657 (mttt) cc_final: 0.8340 (tttp) REVERT: C 340 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.6936 (t60) REVERT: C 542 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6019 (m-10) REVERT: C 547 TRP cc_start: 0.6628 (m100) cc_final: 0.4918 (m100) REVERT: C 675 MET cc_start: 0.8291 (tpt) cc_final: 0.7658 (tpp) REVERT: C 801 MET cc_start: 0.7454 (ttp) cc_final: 0.7221 (ttm) REVERT: D 309 SER cc_start: 0.8318 (p) cc_final: 0.7895 (m) outliers start: 62 outliers final: 39 residues processed: 233 average time/residue: 0.1233 time to fit residues: 49.0206 Evaluate side-chains 219 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 87 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 129 HIS ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.136155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103790 restraints weight = 64660.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.099309 restraints weight = 59082.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100390 restraints weight = 50337.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101852 restraints weight = 40418.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.101632 restraints weight = 34508.926| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23068 Z= 0.151 Angle : 0.586 14.245 31412 Z= 0.289 Chirality : 0.041 0.144 3699 Planarity : 0.003 0.051 3988 Dihedral : 4.192 33.753 3226 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.69 % Allowed : 18.36 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2980 helix: 1.27 (0.15), residues: 1295 sheet: -1.84 (0.24), residues: 437 loop : -1.64 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 351 TYR 0.017 0.001 TYR C 554 PHE 0.021 0.001 PHE C 549 TRP 0.021 0.001 TRP D 641 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (23059) covalent geometry : angle 0.58581 / 0.29 (31396) SS BOND : bond 0.00281 / 0.14 ( 8) SS BOND : angle 0.91633 / 0.46 ( 16) hydrogen bonds : bond 0.03014 / 2.05 ( 958) hydrogen bonds : angle 4.20940 / 2.95 ( 2808) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 ARG cc_start: 0.8414 (ptt180) cc_final: 0.8128 (ptt180) REVERT: B 234 MET cc_start: 0.8539 (tpp) cc_final: 0.8247 (tpp) REVERT: B 248 MET cc_start: 0.8393 (mmm) cc_final: 0.8067 (mmm) REVERT: B 316 MET cc_start: 0.8655 (mmm) cc_final: 0.8430 (mmm) REVERT: C 204 LYS cc_start: 0.8621 (mttt) cc_final: 0.8225 (tptt) REVERT: C 307 MET cc_start: 0.8227 (tpp) cc_final: 0.7959 (tpp) REVERT: C 340 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.6984 (t60) REVERT: C 542 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6733 (m-10) REVERT: C 675 MET cc_start: 0.8080 (tpt) cc_final: 0.7428 (tpp) REVERT: C 801 MET cc_start: 0.7641 (ttp) cc_final: 0.7372 (mtp) REVERT: D 309 SER cc_start: 0.8290 (p) cc_final: 0.7925 (m) outliers start: 62 outliers final: 45 residues processed: 234 average time/residue: 0.1249 time to fit residues: 49.0969 Evaluate side-chains 216 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 163 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 251 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS C 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.137686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104942 restraints weight = 63588.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.100055 restraints weight = 58528.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101228 restraints weight = 51287.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101425 restraints weight = 44383.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101680 restraints weight = 40557.848| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23068 Z= 0.102 Angle : 0.570 14.292 31412 Z= 0.277 Chirality : 0.040 0.142 3699 Planarity : 0.003 0.053 3988 Dihedral : 3.991 33.453 3226 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.34 % Allowed : 19.10 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2980 helix: 1.45 (0.15), residues: 1293 sheet: -1.70 (0.24), residues: 435 loop : -1.55 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 351 TYR 0.019 0.001 TYR C 554 PHE 0.025 0.001 PHE C 820 TRP 0.054 0.001 TRP B 799 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (23059) covalent geometry : angle 0.56990 / 0.28 (31396) SS BOND : bond 0.00238 / 0.11 ( 8) SS BOND : angle 1.00619 / 0.52 ( 16) hydrogen bonds : bond 0.02741 / 1.87 ( 958) hydrogen bonds : angle 4.03004 / 2.83 ( 2808) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 MET cc_start: 0.8316 (tpp) cc_final: 0.8033 (tpp) REVERT: B 248 MET cc_start: 0.8379 (mmm) cc_final: 0.8025 (mmm) REVERT: B 572 LEU cc_start: 0.9445 (mt) cc_final: 0.9142 (pp) REVERT: C 204 LYS cc_start: 0.8648 (mttt) cc_final: 0.8319 (tttp) REVERT: C 340 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.6963 (t60) REVERT: C 542 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: C 675 MET cc_start: 0.8189 (tpt) cc_final: 0.7542 (tpp) REVERT: C 801 MET cc_start: 0.7624 (ttp) cc_final: 0.7411 (mtp) REVERT: D 309 SER cc_start: 0.8356 (p) cc_final: 0.7957 (m) REVERT: D 648 ILE cc_start: 0.9059 (tt) cc_final: 0.8772 (tp) outliers start: 54 outliers final: 41 residues processed: 232 average time/residue: 0.1283 time to fit residues: 49.7276 Evaluate side-chains 217 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 209 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 ASN C 312 HIS C 342 HIS C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.135329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.104100 restraints weight = 64307.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.101872 restraints weight = 61210.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.103078 restraints weight = 52978.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103107 restraints weight = 37993.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.103142 restraints weight = 37618.749| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 23068 Z= 0.191 Angle : 0.644 12.947 31412 Z= 0.317 Chirality : 0.042 0.155 3699 Planarity : 0.004 0.050 3988 Dihedral : 4.327 35.165 3226 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.47 % Allowed : 19.23 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2980 helix: 1.27 (0.15), residues: 1295 sheet: -1.74 (0.24), residues: 446 loop : -1.59 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 351 TYR 0.017 0.001 TYR A 76 PHE 0.027 0.001 PHE C 549 TRP 0.031 0.002 TRP B 799 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (23059) covalent geometry : angle 0.64323 / 0.32 (31396) SS BOND : bond 0.00378 / 0.18 ( 8) SS BOND : angle 1.07457 / 0.53 ( 16) hydrogen bonds : bond 0.03315 / 2.27 ( 958) hydrogen bonds : angle 4.29471 / 3.02 ( 2808) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8280 (tpp) cc_final: 0.8060 (tpp) REVERT: B 248 MET cc_start: 0.8426 (mmm) cc_final: 0.8172 (mmm) REVERT: C 204 LYS cc_start: 0.8572 (mttt) cc_final: 0.8247 (tppt) REVERT: C 340 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7014 (t60) REVERT: C 542 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: C 675 MET cc_start: 0.7548 (tpt) cc_final: 0.6956 (tpp) REVERT: D 309 SER cc_start: 0.8258 (p) cc_final: 0.7913 (m) REVERT: D 648 ILE cc_start: 0.9027 (tt) cc_final: 0.8715 (tp) outliers start: 57 outliers final: 44 residues processed: 232 average time/residue: 0.1210 time to fit residues: 47.6088 Evaluate side-chains 224 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 694 PHE Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 262 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 159 optimal weight: 0.0030 chunk 231 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS C 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.137145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104621 restraints weight = 64335.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.100206 restraints weight = 57969.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101612 restraints weight = 52456.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.101850 restraints weight = 42126.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102046 restraints weight = 37938.663| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23068 Z= 0.112 Angle : 0.601 12.761 31412 Z= 0.291 Chirality : 0.041 0.226 3699 Planarity : 0.003 0.054 3988 Dihedral : 4.104 35.213 3226 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.04 % Allowed : 20.23 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2980 helix: 1.41 (0.15), residues: 1297 sheet: -1.73 (0.25), residues: 423 loop : -1.50 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 289 TYR 0.018 0.001 TYR C 554 PHE 0.017 0.001 PHE B 643 TRP 0.024 0.001 TRP B 799 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (23059) covalent geometry : angle 0.60097 / 0.29 (31396) SS BOND : bond 0.00219 / 0.10 ( 8) SS BOND : angle 1.00365 / 0.49 ( 16) hydrogen bonds : bond 0.02908 / 1.99 ( 958) hydrogen bonds : angle 4.09593 / 2.89 ( 2808) Misc. bond : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.8547 (mmm) cc_final: 0.8301 (mmm) REVERT: B 735 PHE cc_start: 0.5778 (t80) cc_final: 0.4591 (t80) REVERT: C 204 LYS cc_start: 0.8635 (mttt) cc_final: 0.8237 (tppt) REVERT: C 340 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.6967 (t60) REVERT: C 542 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: C 675 MET cc_start: 0.8144 (tpt) cc_final: 0.7465 (tpp) REVERT: C 824 MET cc_start: 0.8394 (ptp) cc_final: 0.8116 (ptp) REVERT: D 309 SER cc_start: 0.8273 (p) cc_final: 0.7904 (m) REVERT: D 648 ILE cc_start: 0.9008 (tt) cc_final: 0.8758 (tp) outliers start: 47 outliers final: 41 residues processed: 213 average time/residue: 0.1201 time to fit residues: 43.2006 Evaluate side-chains 217 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 443 TYR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 210 optimal weight: 0.0060 chunk 152 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 289 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105636 restraints weight = 64476.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100509 restraints weight = 60821.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.102012 restraints weight = 53375.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.102197 restraints weight = 42175.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.102436 restraints weight = 39376.998| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23068 Z= 0.104 Angle : 0.582 12.915 31412 Z= 0.281 Chirality : 0.040 0.176 3699 Planarity : 0.003 0.054 3988 Dihedral : 3.941 35.077 3226 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 20.49 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2980 helix: 1.53 (0.15), residues: 1301 sheet: -1.66 (0.26), residues: 416 loop : -1.37 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.018 0.001 TYR C 554 PHE 0.029 0.001 PHE C 549 TRP 0.019 0.001 TRP D 641 HIS 0.003 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (23059) covalent geometry : angle 0.58221 / 0.28 (31396) SS BOND : bond 0.00234 / 0.11 ( 8) SS BOND : angle 0.94331 / 0.46 ( 16) hydrogen bonds : bond 0.02743 / 1.87 ( 958) hydrogen bonds : angle 4.00953 / 2.83 ( 2808) Misc. bond : bond 0.00063 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.12 seconds wall clock time: 62 minutes 41.87 seconds (3761.87 seconds total)