Starting phenix.real_space_refine on Fri Jun 5 16:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.cif Found real_map, /net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9osg_70806/06_2026/9osg_70806.map" } resolution = 3.83 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= 0.020 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 94 5.16 5 C 13892 2.51 5 N 3678 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s 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: 21712 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5462 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 715} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 578 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 11, 'ARG:plan': 20, 'PHE:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 15, 'TYR:plan': 4, 'ASP:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 305 Chain: "B" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5398 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 727} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 614 Unresolved non-hydrogen angles: 763 Unresolved non-hydrogen dihedrals: 513 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASN:plan1': 7, 'ARG:plan': 14, 'GLU:plan': 20, 'PHE:plan': 7, 'ASP:plan': 17, 'TYR:plan': 5, 'GLN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 350 Chain: "C" Number of atoms: 5170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5170 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 28, 'TRANS': 714} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 987 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASN:plan1': 15, 'GLU:plan': 23, 'ARG:plan': 24, 'PHE:plan': 12, 'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 9, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 518 Chain: "D" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5682 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 726} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 8, 'GLU:plan': 15, 'ASP:plan': 12, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 197 Time building chain proxies: 5.07, per 1000 atoms: 0.23 Number of scatterers: 21712 At special positions: 0 Unit cell: (117.576, 166.14, 199.368, 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 94 16.00 O 4048 8.00 N 3678 7.00 C 13892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 170 " distance=2.02 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 788 " 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=2.04 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=2.02 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=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.3 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 44.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.882A pdb=" N THR A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 80 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.568A pdb=" N SER A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.567A pdb=" N VAL A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.504A pdb=" N ARG A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.502A pdb=" N ARG A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.561A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.630A pdb=" N LEU A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.519A pdb=" N LEU A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.721A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.935A 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 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.703A pdb=" N GLY A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.648A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 removed outlier: 3.593A pdb=" N PHE A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 647 removed outlier: 4.029A pdb=" N ILE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 4.222A pdb=" N ALA A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.686A pdb=" N THR A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 696 removed outlier: 4.084A pdb=" N MET A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 700 removed outlier: 4.005A 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 removed outlier: 4.031A pdb=" N ALA A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.155A pdb=" N TYR A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.534A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 removed outlier: 4.094A pdb=" N LYS A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 829 removed outlier: 4.030A pdb=" N GLY A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.685A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.566A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.927A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.941A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 234 through 244 removed outlier: 3.975A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.600A 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 removed outlier: 3.536A pdb=" N SER B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.550A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.731A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.548A pdb=" N ASP B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.748A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 662 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.721A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.890A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.522A pdb=" N ASP B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.806A pdb=" N LEU B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.541A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 4.049A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 4.106A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.778A pdb=" N MET B 793 " --> pdb=" O GLY B 789 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 845 removed outlier: 3.781A pdb=" N PHE B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 54 removed outlier: 3.537A pdb=" N ALA C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.759A pdb=" N THR C 79 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 80 " --> pdb=" O TYR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.822A pdb=" N SER C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) 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 208 removed outlier: 3.572A pdb=" N ARG C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 232 removed outlier: 3.517A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.897A pdb=" N ILE C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.502A pdb=" N ARG C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 322 removed outlier: 3.924A pdb=" N VAL C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 316 " --> pdb=" O HIS C 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 removed outlier: 3.576A pdb=" N LEU C 346 " --> pdb=" O HIS C 342 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 441 removed outlier: 3.759A pdb=" N GLU C 441 " --> pdb=" O SER C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.783A pdb=" N LEU C 451 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.168A 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 removed outlier: 3.560A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 509 " --> pdb=" O GLU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 566 removed outlier: 3.849A 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 removed outlier: 3.919A pdb=" N GLN C 661 " --> pdb=" O ASP C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 680 removed outlier: 3.646A pdb=" N PHE C 677 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 694 Processing helix chain 'C' and resid 704 through 715 removed outlier: 4.276A pdb=" N ALA C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 711 " --> pdb=" O GLU C 707 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 removed outlier: 4.304A pdb=" N TYR C 728 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS C 729 " --> pdb=" O MET C 725 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 731 " --> pdb=" O GLU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 772 removed outlier: 3.732A pdb=" N THR C 763 " --> pdb=" O ARG C 759 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 783 removed outlier: 3.871A pdb=" N ILE C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 779 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 780 " --> pdb=" O GLU C 776 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 782 " --> pdb=" O LEU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 829 removed outlier: 4.298A pdb=" N PHE C 808 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.554A pdb=" N VAL D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.686A pdb=" N ALA D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.728A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.615A pdb=" N ILE D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (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 244 removed outlier: 3.515A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.750A 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 298 removed outlier: 4.266A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.606A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.887A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.715A pdb=" N ARG D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.746A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.670A pdb=" N LEU D 556 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 581 removed outlier: 4.741A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 566 " --> pdb=" O ASP D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 661 Processing helix chain 'D' and resid 672 through 677 removed outlier: 3.909A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.918A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.591A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.767A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 729 " --> pdb=" O ILE D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.965A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.986A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 845 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 69 removed outlier: 5.744A pdb=" N LEU A 24 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 66 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET A 26 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N PHE A 68 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA A 28 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER A 92 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG A 25 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU A 94 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 27 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.426A pdb=" N ILE A 164 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 214 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE A 267 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LEU A 244 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 266 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 389 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.910A pdb=" N GLU A 363 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.212A pdb=" N VAL A 419 " --> pdb=" O ARG A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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 511 through 512 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 524 removed outlier: 6.538A pdb=" N GLU A 665 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 720 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 667 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N GLU A 722 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 83 removed outlier: 6.707A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N PHE B 107 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY B 39 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AB1, first strand: chain 'B' and resid 368 through 369 removed outlier: 3.733A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.676A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 435 through 436 removed outlier: 6.635A pdb=" N LEU B 512 " --> pdb=" O THR B 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB5, first strand: chain 'B' and resid 490 through 492 removed outlier: 3.603A pdb=" N ALA B 490 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB7, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.649A pdb=" N LYS B 762 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.745A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 62 through 69 removed outlier: 3.610A pdb=" N PHE C 68 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 92 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 93 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.957A pdb=" N SER C 189 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER C 162 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP C 217 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 164 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR C 242 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE C 264 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 389 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU C 379 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLU C 387 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.981A pdb=" N GLU C 363 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 420 through 421 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 511 through 512 Processing sheet with id=AC6, first strand: chain 'C' and resid 719 through 722 removed outlier: 4.529A pdb=" N ILE C 523 " --> pdb=" O ILE C 739 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 739 " --> pdb=" O ILE C 523 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.777A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.908A pdb=" N THR D 171 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE D 227 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.622A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 477 through 480 removed outlier: 6.656A pdb=" N LEU D 512 " --> pdb=" O THR D 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 444 through 446 Processing sheet with id=AD3, first strand: chain 'D' and resid 490 through 492 removed outlier: 3.534A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD5, first strand: chain 'D' and resid 534 through 535 removed outlier: 3.710A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 683 through 684 removed outlier: 7.466A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3557 1.27 - 1.41: 5418 1.41 - 1.55: 12963 1.55 - 1.69: 25 1.69 - 1.83: 160 Bond restraints: 22123 Sorted by residual: bond pdb=" C PRO C 515 " pdb=" O PRO C 515 " ideal model delta sigma weight residual 1.235 1.130 0.105 1.30e-02 5.92e+03 6.51e+01 bond pdb=" C PRO B 532 " pdb=" O PRO B 532 " ideal model delta sigma weight residual 1.233 1.140 0.093 1.39e-02 5.18e+03 4.50e+01 bond pdb=" CA ILE B 519 " pdb=" C ILE B 519 " ideal model delta sigma weight residual 1.527 1.462 0.064 9.70e-03 1.06e+04 4.41e+01 bond pdb=" C MET B 276 " pdb=" O MET B 276 " ideal model delta sigma weight residual 1.235 1.157 0.078 1.18e-02 7.18e+03 4.35e+01 bond pdb=" C PHE C 516 " pdb=" O PHE C 516 " ideal model delta sigma weight residual 1.235 1.147 0.088 1.38e-02 5.25e+03 4.03e+01 ... (remaining 22118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28614 2.46 - 4.91: 1322 4.91 - 7.37: 174 7.37 - 9.82: 48 9.82 - 12.28: 11 Bond angle restraints: 30169 Sorted by residual: angle pdb=" N ALA A 564 " pdb=" CA ALA A 564 " pdb=" C ALA A 564 " ideal model delta sigma weight residual 111.28 123.56 -12.28 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N GLU A 802 " pdb=" CA GLU A 802 " pdb=" C GLU A 802 " ideal model delta sigma weight residual 111.02 123.22 -12.20 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N LEU A 615 " pdb=" CA LEU A 615 " pdb=" C LEU A 615 " ideal model delta sigma weight residual 111.28 120.99 -9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" N LEU A 799 " pdb=" CA LEU A 799 " pdb=" C LEU A 799 " ideal model delta sigma weight residual 112.92 102.20 10.72 1.23e+00 6.61e-01 7.60e+01 angle pdb=" C SER B 666 " pdb=" N PRO B 667 " pdb=" CA PRO B 667 " ideal model delta sigma weight residual 120.11 129.87 -9.76 1.12e+00 7.97e-01 7.59e+01 ... (remaining 30164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11893 17.84 - 35.67: 955 35.67 - 53.51: 186 53.51 - 71.35: 29 71.35 - 89.18: 14 Dihedral angle restraints: 13077 sinusoidal: 4377 harmonic: 8700 Sorted by residual: dihedral pdb=" CB CYS A 734 " pdb=" SG CYS A 734 " pdb=" SG CYS A 788 " pdb=" CB CYS A 788 " ideal model delta sinusoidal sigma weight residual 93.00 175.29 -82.29 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" C ARG B 634 " pdb=" N ARG B 634 " pdb=" CA ARG B 634 " pdb=" CB ARG B 634 " ideal model delta harmonic sigma weight residual -122.60 -142.01 19.41 0 2.50e+00 1.60e-01 6.03e+01 dihedral pdb=" C TRP D 564 " pdb=" N TRP D 564 " pdb=" CA TRP D 564 " pdb=" CB TRP D 564 " ideal model delta harmonic sigma weight residual -122.60 -141.40 18.80 0 2.50e+00 1.60e-01 5.65e+01 ... (remaining 13074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 3446 0.155 - 0.309: 160 0.309 - 0.464: 12 0.464 - 0.618: 2 0.618 - 0.773: 2 Chirality restraints: 3622 Sorted by residual: chirality pdb=" CA ARG B 634 " pdb=" N ARG B 634 " pdb=" C ARG B 634 " pdb=" CB ARG B 634 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA TRP D 564 " pdb=" N TRP D 564 " pdb=" C TRP D 564 " pdb=" CB TRP D 564 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA ASN D 654 " pdb=" N ASN D 654 " pdb=" C ASN D 654 " pdb=" CB ASN D 654 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 3619 not shown) Planarity restraints: 3839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 414 " -0.027 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ASN C 414 " 0.092 2.00e-02 2.50e+03 pdb=" O ASN C 414 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS C 415 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 818 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C GLN D 818 " -0.071 2.00e-02 2.50e+03 pdb=" O GLN D 818 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN D 819 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 837 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C VAL B 837 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL B 837 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 838 " 0.023 2.00e-02 2.50e+03 ... (remaining 3836 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 106 2.53 - 3.12: 15629 3.12 - 3.71: 31443 3.71 - 4.31: 42132 4.31 - 4.90: 70866 Nonbonded interactions: 160176 Sorted by model distance: nonbonded pdb=" CB SER B 711 " pdb=" O LEU C 743 " model vdw 1.936 3.440 nonbonded pdb=" O VAL A 560 " pdb=" CB ALA A 564 " model vdw 2.080 2.768 nonbonded pdb=" O GLY B 551 " pdb=" O SER B 554 " model vdw 2.157 3.040 nonbonded pdb=" O ALA A 813 " pdb=" CG1 ILE A 816 " model vdw 2.226 3.440 nonbonded pdb=" O LEU A 658 " pdb=" N GLN A 661 " model vdw 2.250 3.120 ... (remaining 160171 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' and (resid 21 through 418 or (resid 419 through 425 and (name N or na \ me CA or name C or name O or name CB )) or resid 426 through 427 or (resid 428 t \ hrough 438 and (name N or name CA or name C or name O or name CB )) or (resid 43 \ 9 through 469 and (name N or name CA or name C or name O or name CB )) or resid \ 470 through 480 or (resid 481 through 482 and (name N or name CA or name C or na \ me O or name CB )) or (resid 483 through 485 and (name N or name CA or name C or \ name O or name CB )) or (resid 486 through 511 and (name N or name CA or name C \ or name O or name CB )) or resid 512 or (resid 513 through 519 and (name N or n \ ame CA or name C or name O or name CB )) or resid 520 through 524 or (resid 525 \ through 529 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 0 through 650 or (resid 651 through 652 and (name N or name CA or name C or name \ O or name CB )) or resid 653 through 659 or (resid 660 through 661 and (name N \ or name CA or name C or name O or name CB )) or resid 662 or (resid 663 and (nam \ e N or name CA or name C or name O or name CB )) or resid 664 or (resid 665 thro \ ugh 666 and (name N or name CA or name C or name O or name CB )) or resid 667 th \ rough 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) \ or resid 676 or (resid 677 through 680 and (name N or name CA or name C or name \ O or name CB )) or resid 681 through 683 or (resid 684 and (name N or name CA o \ r name C or name O or name CB )) or resid 685 through 686 or (resid 687 through \ 694 and (name N or name CA or name C or name O or name CB )) or resid 695 throug \ h 710 or (resid 711 and (name N or name CA or name C or name O or name CB )) or \ resid 712 through 716 or (resid 717 through 719 and (name N or name CA or name C \ or name O or name CB )) or resid 720 through 721 or (resid 722 and (name N or n \ ame CA or name C or name O or name CB )) or resid 723 through 725 or (resid 726 \ through 731 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 2 through 737 or (resid 738 and (name N or name CA or name C or name O or name C \ B )) or resid 739 through 745 or (resid 746 and (name N or name CA or name C or \ name O or name CB )) or resid 747 or (resid 748 and (name N or name CA or name C \ or name O or name CB )) or resid 749 through 752 or (resid 753 and (name N or n \ ame CA or name C or name O or name CB )) or resid 754 through 757 or (resid 758 \ through 761 and (name N or name CA or name C or name O or name CB )) or resid 76 \ 2 through 769 or (resid 770 through 774 and (name N or name CA or name C or name \ O or name CB )) or resid 775 or (resid 776 and (name N or name CA or name C or \ name O or name CB )) or resid 777 through 778 or (resid 779 through 784 and (nam \ e N or name CA or name C or name O or name CB )) or resid 785 through 798 or (re \ sid 799 and (name N or name CA or name C or name O or name CB )) or resid 800 th \ rough 829)) selection = (chain 'C' and (resid 21 through 470 or (resid 471 and (name N or name CA or nam \ e C or name O or name CB )) or resid 472 through 560 or (resid 561 through 614 a \ nd (name N or name CA or name C or name O or name CB )) or resid 615 through 802 \ or (resid 803 through 804 and (name N or name CA or name C or name O or name CB \ )) or resid 805 through 827 or (resid 828 through 829 and (name N or name CA or \ name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 33 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 through 561 or (resid 562 and (name N o \ r name CA or name C or name O or name CB )) or resid 563 through 568 or (resid 5 \ 69 through 570 and (name N or name CA or name C or name O or name CB )) or resid \ 571 through 704 or (resid 705 and (name N or name CA or name C or name O or nam \ e CB )) or resid 706 through 726 or (resid 727 and (name N or name CA or name C \ or name O or name CB )) or resid 728 through 742 or (resid 743 and (name N or na \ me CA or name C or name O or name CB )) or resid 744 through 746 or (resid 747 t \ hrough 748 and (name N or name CA or name C or name O or name CB )) or resid 749 \ through 750 or (resid 751 and (name N or name CA or name C or name O or name CB \ )) or resid 752 through 831 or (resid 832 and (name N or name CA or name C or n \ ame O or name CB )) or resid 833 through 835 or (resid 836 and (name N or name C \ A or name C or name O or name CB )) or resid 837 through 840 or (resid 841 throu \ gh 842 and (name N or name CA or name C or name O or name CB )) or resid 843 or \ (resid 844 through 845 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'D' and (resid 33 through 431 or (resid 432 through 442 and (name N or na \ me CA or name C or name O or name CB )) or resid 443 or (resid 444 through 454 a \ nd (name N or name CA or name C or name O or name CB )) or resid 455 or (resid 4 \ 56 through 460 and (name N or name CA or name C or name O or name CB )) or resid \ 461 through 463 or (resid 464 through 474 and (name N or name CA or name C or n \ ame O or name CB )) or resid 475 or (resid 476 through 485 and (name N or name C \ A or name C or name O or name CB )) or (resid 486 through 488 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 489 through 499 and (name N or \ name CA or name C or name O or name CB )) or resid 500 or (resid 501 through 515 \ and (name N or name CA or name C or name O or name CB )) or resid 516 or (resid \ 517 through 518 and (name N or name CA or name C or name O or name CB )) or res \ id 519 through 520 or (resid 521 through 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 or (resid 530 through 532 and (name N or name \ CA or name C or name O or name CB )) or resid 533 through 543 or (resid 544 and \ (name N or name CA or name C or name O or name CB )) or resid 545 or (resid 546 \ and (name N or name CA or name C or name O or name CB )) or (resid 547 through \ 550 and (name N or name CA or name C or name O or name CB )) or resid 551 or (re \ sid 552 through 554 and (name N or name CA or name C or name O or name CB )) or \ resid 555 through 567 or (resid 568 through 570 and (name N or name CA or name C \ or name O or name CB )) or resid 571 or (resid 572 and (name N or name CA or na \ me C or name O or name CB )) or resid 573 through 574 or (resid 575 and (name N \ or name CA or name C or name O or name CB )) or resid 576 through 578 or (resid \ 579 through 630 and (name N or name CA or name C or name O or name CB )) or resi \ d 631 through 633 or (resid 634 and (name N or name CA or name C or name O or na \ me CB )) or resid 635 through 661 or (resid 662 through 663 and (name N or name \ CA or name C or name O or name CB )) or resid 664 through 666 or (resid 667 and \ (name N or name CA or name C or name O or name CB )) or resid 668 through 672 or \ (resid 673 and (name N or name CA or name C or name O or name CB )) or resid 67 \ 4 through 675 or (resid 676 through 677 and (name N or name CA or name C or name \ O or name CB )) or resid 678 through 702 or (resid 703 through 705 and (name N \ or name CA or name C or name O or name CB )) or resid 706 through 707 or (resid \ 708 through 709 and (name N or name CA or name C or name O or name CB )) or resi \ d 710 through 768 or (resid 769 through 770 and (name N or name CA or name C or \ name O or name CB )) or resid 771 through 772 or (resid 773 through 777 and (nam \ e N or name CA or name C or name O or name CB )) or resid 778 through 783 or (re \ sid 784 and (name N or name CA or name C or name O or name CB )) or resid 785 or \ (resid 786 through 788 and (name N or name CA or name C or name O or name CB )) \ or resid 789 or (resid 790 and (name N or name CA or name C or name O or name C \ B )) or resid 791 or (resid 792 through 797 and (name N or name CA or name C or \ name O or name CB )) or resid 798 through 845)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.790 Find NCS groups from input model: 0.600 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 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 : 0.010 0.105 22132 Z= 0.612 Angle : 1.220 12.280 30187 Z= 0.803 Chirality : 0.076 0.773 3622 Planarity : 0.007 0.088 3839 Dihedral : 13.868 89.182 7434 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.46 % Favored : 90.37 % Rotamer: Outliers : 1.70 % Allowed : 9.23 % Favored : 89.07 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -5.30 (0.11), residues: 2980 helix: -4.34 (0.07), residues: 1234 sheet: -1.90 (0.24), residues: 402 loop : -3.10 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 220 TYR 0.046 0.003 TYR C 427 PHE 0.038 0.002 PHE B 533 TRP 0.019 0.002 TRP B 296 HIS 0.013 0.002 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.01029 / 0.61 (22123) covalent geometry : angle 1.21808 / 0.80 (30169) SS BOND : bond 0.00753 / 0.36 ( 9) SS BOND : angle 2.92152 / 1.57 ( 18) hydrogen bonds : bond 0.28378 / 19.20 ( 864) hydrogen bonds : angle 9.44944 / 6.43 ( 2502) *********************** 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 439 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 404 time to evaluate : 0.719 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: B 50 MET cc_start: 0.5422 (mtp) cc_final: 0.5108 (mtm) REVERT: B 147 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9201 (m) REVERT: C 297 TYR cc_start: 0.7736 (t80) cc_final: 0.7534 (t80) REVERT: D 223 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6917 (mt-10) REVERT: D 388 ASP cc_start: 0.7990 (m-30) cc_final: 0.7482 (p0) outliers start: 35 outliers final: 6 residues processed: 430 average time/residue: 0.1569 time to fit residues: 101.8390 Evaluate side-chains 216 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 659 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 342 HIS B 73 ASN B 129 HIS B 253 HIS B 557 ASN B 819 ASN C 322 ASN C 325 GLN D 98 GLN D 129 HIS D 367 HIS D 654 ASN ** D 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.180872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162409 restraints weight = 41211.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.157499 restraints weight = 67385.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155689 restraints weight = 73833.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154883 restraints weight = 74752.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153284 restraints weight = 64488.957| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22132 Z= 0.149 Angle : 0.614 8.037 30187 Z= 0.329 Chirality : 0.042 0.207 3622 Planarity : 0.005 0.064 3839 Dihedral : 4.868 26.104 3201 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 2.04 % Allowed : 14.09 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -3.50 (0.13), residues: 2980 helix: -2.19 (0.12), residues: 1267 sheet: -1.52 (0.25), residues: 379 loop : -2.63 (0.14), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 173 TYR 0.018 0.001 TYR A 297 PHE 0.019 0.001 PHE A 627 TRP 0.016 0.001 TRP D 564 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (22123) covalent geometry : angle 0.61182 / 0.33 (30169) SS BOND : bond 0.00571 / 0.34 ( 9) SS BOND : angle 2.26217 / 1.34 ( 18) hydrogen bonds : bond 0.05367 / 3.67 ( 864) hydrogen bonds : angle 5.03611 / 3.44 ( 2502) *********************** 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 282 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 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: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2830 (ptt) cc_final: 0.1397 (mmp) REVERT: A 666 TYR cc_start: 0.4155 (t80) cc_final: 0.3884 (t80) REVERT: B 248 MET cc_start: 0.8737 (mmm) cc_final: 0.8465 (mtp) REVERT: B 660 THR cc_start: 0.8089 (m) cc_final: 0.7610 (t) REVERT: C 361 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6667 (mtp180) REVERT: C 619 ILE cc_start: 0.8269 (pt) cc_final: 0.7970 (mm) REVERT: D 50 MET cc_start: 0.5740 (mtp) cc_final: 0.5497 (mtm) REVERT: D 58 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6272 (mtm-85) REVERT: D 141 ASN cc_start: 0.7350 (t0) cc_final: 0.6957 (p0) REVERT: D 153 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8452 (t80) REVERT: D 388 ASP cc_start: 0.8211 (m-30) cc_final: 0.7544 (p0) REVERT: D 501 MET cc_start: 0.1987 (mmm) cc_final: 0.1689 (mmp) outliers start: 42 outliers final: 14 residues processed: 276 average time/residue: 0.1452 time to fit residues: 62.6852 Evaluate side-chains 214 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 137 optimal weight: 30.0000 chunk 140 optimal weight: 0.0570 chunk 85 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 638 ASN A 694 GLN B 328 HIS C 342 HIS ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 749 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.177458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.160203 restraints weight = 40841.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155089 restraints weight = 63382.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152985 restraints weight = 66210.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.152241 restraints weight = 74566.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151280 restraints weight = 68750.565| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22132 Z= 0.170 Angle : 0.591 8.468 30187 Z= 0.311 Chirality : 0.042 0.176 3622 Planarity : 0.004 0.055 3839 Dihedral : 4.419 21.685 3193 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 15.99 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -2.15 (0.14), residues: 2980 helix: -0.60 (0.14), residues: 1286 sheet: -1.35 (0.25), residues: 414 loop : -2.29 (0.15), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 647 TYR 0.028 0.002 TYR B 566 PHE 0.031 0.002 PHE B 642 TRP 0.023 0.001 TRP A 625 HIS 0.008 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22123) covalent geometry : angle 0.59020 / 0.31 (30169) SS BOND : bond 0.00483 / 0.21 ( 9) SS BOND : angle 1.62230 / 0.91 ( 18) hydrogen bonds : bond 0.04166 / 2.84 ( 864) hydrogen bonds : angle 4.29647 / 2.93 ( 2502) *********************** 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 253 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2749 (ptt) cc_final: 0.1289 (mmp) REVERT: B 301 LEU cc_start: 0.6035 (mt) cc_final: 0.5747 (mt) REVERT: D 388 ASP cc_start: 0.8097 (m-30) cc_final: 0.7471 (p0) REVERT: D 501 MET cc_start: 0.2393 (mmm) cc_final: 0.1997 (mmp) outliers start: 48 outliers final: 22 residues processed: 246 average time/residue: 0.1296 time to fit residues: 51.6880 Evaluate side-chains 203 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 335 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 59 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 50.0000 chunk 221 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 173 optimal weight: 0.0970 chunk 267 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS A 638 ASN A 687 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS D 123 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS D 677 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.174153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156663 restraints weight = 40611.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.152597 restraints weight = 69848.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.151034 restraints weight = 57632.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149852 restraints weight = 62620.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147717 restraints weight = 63534.635| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22132 Z= 0.224 Angle : 0.620 7.838 30187 Z= 0.326 Chirality : 0.043 0.162 3622 Planarity : 0.004 0.054 3839 Dihedral : 4.487 20.866 3193 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.79 % Allowed : 16.57 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -1.60 (0.15), residues: 2980 helix: -0.01 (0.15), residues: 1288 sheet: -1.24 (0.25), residues: 420 loop : -2.07 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 361 TYR 0.018 0.002 TYR D 324 PHE 0.032 0.002 PHE B 642 TRP 0.020 0.002 TRP D 564 HIS 0.005 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (22123) covalent geometry : angle 0.61878 / 0.33 (30169) SS BOND : bond 0.00637 / 0.30 ( 9) SS BOND : angle 1.77930 / 1.06 ( 18) hydrogen bonds : bond 0.04164 / 2.86 ( 864) hydrogen bonds : angle 4.26639 / 2.91 ( 2502) *********************** 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 283 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2867 (ptt) cc_final: 0.1549 (mmp) REVERT: B 53 GLU cc_start: 0.8396 (mp0) cc_final: 0.8194 (mt-10) REVERT: B 301 LEU cc_start: 0.5971 (mt) cc_final: 0.5719 (mt) REVERT: C 129 GLN cc_start: 0.6707 (pm20) cc_final: 0.6463 (mm-40) REVERT: C 321 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (tt) REVERT: C 361 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6583 (mtp180) REVERT: D 153 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8668 (t80) REVERT: D 388 ASP cc_start: 0.8016 (m-30) cc_final: 0.7368 (p0) REVERT: D 501 MET cc_start: 0.2526 (mmm) cc_final: 0.2142 (mmt) outliers start: 78 outliers final: 44 residues processed: 274 average time/residue: 0.1313 time to fit residues: 58.1650 Evaluate side-chains 226 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 286 optimal weight: 8.9990 chunk 115 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS A 638 ASN B 98 GLN B 348 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D 335 GLN ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.174847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.157910 restraints weight = 40271.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.152894 restraints weight = 64649.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.151074 restraints weight = 70772.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150331 restraints weight = 74699.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148620 restraints weight = 65335.218| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22132 Z= 0.159 Angle : 0.572 8.654 30187 Z= 0.297 Chirality : 0.042 0.170 3622 Planarity : 0.004 0.054 3839 Dihedral : 4.247 22.876 3193 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 3.45 % Allowed : 17.98 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -1.17 (0.15), residues: 2980 helix: 0.48 (0.15), residues: 1277 sheet: -1.10 (0.26), residues: 405 loop : -1.96 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 361 TYR 0.017 0.002 TYR C 130 PHE 0.025 0.001 PHE B 642 TRP 0.018 0.001 TRP A 625 HIS 0.019 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (22123) covalent geometry : angle 0.56959 / 0.30 (30169) SS BOND : bond 0.00785 / 0.42 ( 9) SS BOND : angle 2.20232 / 1.31 ( 18) hydrogen bonds : bond 0.03546 / 2.44 ( 864) hydrogen bonds : angle 4.01734 / 2.75 ( 2502) *********************** 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 261 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 190 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2856 (ptt) cc_final: 0.1540 (mmt) REVERT: A 687 GLN cc_start: 0.5229 (OUTLIER) cc_final: 0.4912 (mp10) REVERT: B 301 LEU cc_start: 0.5936 (mt) cc_final: 0.5725 (mt) REVERT: B 348 ASN cc_start: 0.7585 (m-40) cc_final: 0.7335 (m-40) REVERT: D 153 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8516 (t80) REVERT: D 365 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: D 388 ASP cc_start: 0.7925 (m-30) cc_final: 0.7362 (p0) REVERT: D 501 MET cc_start: 0.2876 (mmm) cc_final: 0.2531 (mmt) outliers start: 71 outliers final: 53 residues processed: 251 average time/residue: 0.1185 time to fit residues: 50.3854 Evaluate side-chains 238 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 218 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 638 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.171734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154161 restraints weight = 40096.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.150116 restraints weight = 66925.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.147943 restraints weight = 57406.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.146273 restraints weight = 68697.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144349 restraints weight = 71579.106| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 22132 Z= 0.285 Angle : 0.657 8.150 30187 Z= 0.342 Chirality : 0.045 0.197 3622 Planarity : 0.004 0.056 3839 Dihedral : 4.539 21.697 3193 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 4.08 % Allowed : 17.49 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -1.18 (0.15), residues: 2980 helix: 0.51 (0.15), residues: 1265 sheet: -1.29 (0.26), residues: 410 loop : -1.91 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 370 TYR 0.034 0.002 TYR C 130 PHE 0.022 0.002 PHE D 337 TRP 0.017 0.002 TRP A 625 HIS 0.006 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.28 (22123) covalent geometry : angle 0.65592 / 0.34 (30169) SS BOND : bond 0.00606 / 0.26 ( 9) SS BOND : angle 1.93533 / 1.17 ( 18) hydrogen bonds : bond 0.04233 / 2.88 ( 864) hydrogen bonds : angle 4.30000 / 2.94 ( 2502) *********************** 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 276 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 192 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 189 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8834 (m) REVERT: A 429 MET cc_start: 0.5063 (ppp) cc_final: 0.4552 (ppp) REVERT: A 450 MET cc_start: 0.2958 (ptt) cc_final: 0.1696 (mmp) REVERT: B 348 ASN cc_start: 0.7628 (m-40) cc_final: 0.7422 (m-40) REVERT: C 321 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8202 (tt) REVERT: C 361 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6700 (mtp180) REVERT: D 153 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8754 (t80) REVERT: D 335 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: D 388 ASP cc_start: 0.8111 (m-30) cc_final: 0.7457 (p0) REVERT: D 501 MET cc_start: 0.2991 (mmm) cc_final: 0.2614 (mmt) outliers start: 84 outliers final: 61 residues processed: 264 average time/residue: 0.1192 time to fit residues: 52.8893 Evaluate side-chains 247 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 690 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 232 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 638 ASN B 98 GLN D 123 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 350 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.175022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.157455 restraints weight = 40172.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.153429 restraints weight = 63470.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150550 restraints weight = 50155.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.148387 restraints weight = 65060.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146696 restraints weight = 67396.405| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22132 Z= 0.113 Angle : 0.533 7.860 30187 Z= 0.278 Chirality : 0.040 0.158 3622 Planarity : 0.004 0.052 3839 Dihedral : 4.035 21.527 3193 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 3.01 % Allowed : 18.76 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -0.71 (0.16), residues: 2980 helix: 0.91 (0.15), residues: 1279 sheet: -1.03 (0.26), residues: 410 loop : -1.71 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 370 TYR 0.035 0.001 TYR C 130 PHE 0.017 0.001 PHE B 642 TRP 0.021 0.001 TRP A 625 HIS 0.003 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (22123) covalent geometry : angle 0.53178 / 0.28 (30169) SS BOND : bond 0.00291 / 0.17 ( 9) SS BOND : angle 1.47652 / 0.89 ( 18) hydrogen bonds : bond 0.03124 / 2.17 ( 864) hydrogen bonds : angle 3.81416 / 2.62 ( 2502) *********************** 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 252 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.4963 (ppp) cc_final: 0.4615 (ppp) REVERT: A 450 MET cc_start: 0.2972 (ptt) cc_final: 0.1715 (mmt) REVERT: D 55 LEU cc_start: 0.8956 (mt) cc_final: 0.8556 (mt) REVERT: D 153 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8385 (t80) REVERT: D 335 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6911 (mt0) REVERT: D 388 ASP cc_start: 0.7908 (m-30) cc_final: 0.7334 (p0) outliers start: 62 outliers final: 45 residues processed: 241 average time/residue: 0.1226 time to fit residues: 49.4564 Evaluate side-chains 225 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET 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 287 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 120 optimal weight: 50.0000 chunk 197 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 206 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 638 ASN A 687 GLN D 111 HIS ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.168693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147857 restraints weight = 39847.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.142238 restraints weight = 68529.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140291 restraints weight = 74102.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138953 restraints weight = 74852.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136675 restraints weight = 69651.621| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 22132 Z= 0.341 Angle : 0.725 8.269 30187 Z= 0.377 Chirality : 0.047 0.194 3622 Planarity : 0.005 0.053 3839 Dihedral : 4.719 25.861 3193 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 3.50 % Allowed : 18.46 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -1.13 (0.15), residues: 2980 helix: 0.60 (0.15), residues: 1282 sheet: -1.46 (0.26), residues: 402 loop : -1.90 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 58 TYR 0.039 0.002 TYR C 130 PHE 0.026 0.003 PHE D 57 TRP 0.015 0.002 TRP A 625 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.34 (22123) covalent geometry : angle 0.72246 / 0.38 (30169) SS BOND : bond 0.00684 / 0.34 ( 9) SS BOND : angle 2.34481 / 1.45 ( 18) hydrogen bonds : bond 0.04608 / 3.13 ( 864) hydrogen bonds : angle 4.44798 / 3.04 ( 2502) *********************** 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 256 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2861 (ptt) cc_final: 0.1838 (mmp) REVERT: A 517 MET cc_start: 0.3456 (pmm) cc_final: 0.2999 (pmm) REVERT: A 782 TRP cc_start: 0.4700 (m100) cc_final: 0.4059 (m100) REVERT: B 348 ASN cc_start: 0.8073 (m-40) cc_final: 0.7840 (m-40) REVERT: C 40 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: D 153 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8658 (t80) REVERT: D 335 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: D 388 ASP cc_start: 0.8043 (m-30) cc_final: 0.7387 (p0) outliers start: 72 outliers final: 59 residues processed: 248 average time/residue: 0.1214 time to fit residues: 50.2639 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 : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 228 optimal weight: 5.9990 chunk 195 optimal weight: 50.0000 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 274 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 638 ASN B 98 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.170945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148656 restraints weight = 39633.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.143071 restraints weight = 69560.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140516 restraints weight = 68512.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139878 restraints weight = 72998.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138165 restraints weight = 63438.053| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22132 Z= 0.192 Angle : 0.615 10.197 30187 Z= 0.319 Chirality : 0.043 0.179 3622 Planarity : 0.004 0.055 3839 Dihedral : 4.392 28.117 3193 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.26 % Allowed : 18.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -0.86 (0.16), residues: 2980 helix: 0.86 (0.15), residues: 1275 sheet: -1.34 (0.26), residues: 407 loop : -1.78 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 58 TYR 0.040 0.002 TYR C 130 PHE 0.023 0.002 PHE A 538 TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (22123) covalent geometry : angle 0.61278 / 0.32 (30169) SS BOND : bond 0.00686 / 0.36 ( 9) SS BOND : angle 2.30206 / 1.41 ( 18) hydrogen bonds : bond 0.03711 / 2.55 ( 864) hydrogen bonds : angle 4.05267 / 2.79 ( 2502) *********************** 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 252 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8438 (mt) REVERT: A 382 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5574 (mtm-85) REVERT: A 429 MET cc_start: 0.5143 (ppp) cc_final: 0.4540 (ppp) REVERT: A 450 MET cc_start: 0.3033 (ptt) cc_final: 0.1860 (mmp) REVERT: A 517 MET cc_start: 0.3268 (pmm) cc_final: 0.2999 (pmm) REVERT: A 782 TRP cc_start: 0.4544 (m100) cc_final: 0.3977 (m100) REVERT: B 348 ASN cc_start: 0.8081 (m-40) cc_final: 0.7751 (m-40) REVERT: C 40 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.5927 (mp0) REVERT: C 82 MET cc_start: 0.8973 (tpp) cc_final: 0.8737 (tpt) REVERT: C 321 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (tt) REVERT: D 153 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8659 (t80) REVERT: D 335 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: D 388 ASP cc_start: 0.7874 (m-30) cc_final: 0.7319 (p0) outliers start: 67 outliers final: 53 residues processed: 247 average time/residue: 0.1216 time to fit residues: 49.3809 Evaluate side-chains 237 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 110 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 239 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 98 GLN C 50 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.173269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150902 restraints weight = 39998.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.145835 restraints weight = 70216.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142834 restraints weight = 70301.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141870 restraints weight = 68420.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139235 restraints weight = 63662.741| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22132 Z= 0.107 Angle : 0.555 9.015 30187 Z= 0.286 Chirality : 0.040 0.173 3622 Planarity : 0.004 0.056 3839 Dihedral : 3.996 26.933 3193 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 2.28 % Allowed : 19.44 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -0.45 (0.16), residues: 2980 helix: 1.23 (0.15), residues: 1269 sheet: -1.00 (0.27), residues: 385 loop : -1.63 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 37 TYR 0.032 0.001 TYR C 130 PHE 0.025 0.001 PHE A 538 TRP 0.024 0.001 TRP C 624 HIS 0.002 0.000 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22123) covalent geometry : angle 0.55342 / 0.28 (30169) SS BOND : bond 0.00286 / 0.15 ( 9) SS BOND : angle 1.86638 / 1.13 ( 18) hydrogen bonds : bond 0.02950 / 2.03 ( 864) hydrogen bonds : angle 3.73638 / 2.57 ( 2502) ********************** 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 233 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 382 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5471 (mtm-85) REVERT: A 450 MET cc_start: 0.3064 (ptt) cc_final: 0.1759 (mmp) REVERT: A 782 TRP cc_start: 0.4605 (m100) cc_final: 0.4068 (m100) REVERT: B 301 LEU cc_start: 0.5222 (mp) cc_final: 0.4687 (mp) REVERT: B 348 ASN cc_start: 0.8074 (m-40) cc_final: 0.7756 (m-40) REVERT: D 388 ASP cc_start: 0.7823 (m-30) cc_final: 0.7302 (p0) outliers start: 47 outliers final: 40 residues processed: 229 average time/residue: 0.1313 time to fit residues: 48.9949 Evaluate side-chains 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET 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 287 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 101 optimal weight: 0.0070 chunk 61 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN B 98 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.172815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155304 restraints weight = 40284.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151743 restraints weight = 70224.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149373 restraints weight = 61683.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.148149 restraints weight = 73237.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.146466 restraints weight = 72912.752| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22132 Z= 0.201 Angle : 0.614 9.805 30187 Z= 0.316 Chirality : 0.043 0.178 3622 Planarity : 0.004 0.055 3839 Dihedral : 4.211 27.710 3193 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.58 % Allowed : 19.29 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.07 % 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: -0.52 (0.16), residues: 2980 helix: 1.18 (0.15), residues: 1272 sheet: -1.22 (0.27), residues: 391 loop : -1.61 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 37 TYR 0.032 0.002 TYR C 130 PHE 0.024 0.002 PHE A 538 TRP 0.022 0.002 TRP A 547 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (22123) covalent geometry : angle 0.61178 / 0.32 (30169) SS BOND : bond 0.00478 / 0.25 ( 9) SS BOND : angle 2.02196 / 1.23 ( 18) hydrogen bonds : bond 0.03550 / 2.42 ( 864) hydrogen bonds : angle 3.99090 / 2.74 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.42 seconds wall clock time: 54 minutes 34.19 seconds (3274.19 seconds total)