Starting phenix.real_space_refine on Sun Sep 13 14:06:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.cif Found real_map, /net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6why_21680/09_2026/6why_21680.cif" } resolution = 4.03 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= 0.017 sd= 0.833 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2138 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 Cl 4 4.86 5 C 14284 2.51 5 N 3626 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22198 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5608 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 33, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 11, 'ARG:plan': 27, 'GLN:plan1': 11, 'PHE:plan': 5, 'TYR:plan': 3, 'HIS:plan': 6, 'ASP:plan': 14, 'GLU:plan': 26} Unresolved non-hydrogen planarities: 439 Chain: "B" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5424 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 26, 'TRANS': 732} Chain breaks: 5 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 5, 'GLU:plan': 27, 'ASN:plan1': 6, 'ARG:plan': 13, 'GLN:plan1': 13, 'TYR:plan': 10, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 404 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, F Time building chain proxies: 9.10, per 1000 atoms: 0.41 Number of scatterers: 22198 At special positions: 0 Unit cell: (141.11, 147.96, 182.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 126 16.00 O 4158 8.00 N 3626 7.00 C 14284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.05 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.01 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.04 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.05 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 903 " - " ASN B 542 " " NAG D 903 " - " ASN D 542 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 976.9 milliseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5792 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 34 sheets defined 43.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 71 through 82 removed outlier: 4.748A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.327A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.521A pdb=" N MET A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.974A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.570A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.654A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 removed outlier: 4.208A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.668A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.658A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 604 removed outlier: 4.096A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.660A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 4.011A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 659 " --> pdb=" O MET A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.747A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 4.899A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.908A pdb=" N GLU A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.509A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 52 through 60 removed outlier: 4.219A pdb=" N LYS B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.043A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.143A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.742A pdb=" N VAL B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.973A pdb=" N ASP B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.576A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.510A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.310A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 4.495A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 578 removed outlier: 4.642A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 614 removed outlier: 3.915A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 651 removed outlier: 3.504A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.936A pdb=" N GLN B 656 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 691 No H-bonds generated for 'chain 'B' and resid 689 through 691' Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.067A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.511A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 784 removed outlier: 3.590A pdb=" N ASP B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 818 through 844 removed outlier: 3.882A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.748A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.327A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.521A pdb=" N MET C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.974A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 298 through 314 removed outlier: 3.569A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 4.654A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 removed outlier: 4.208A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.668A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 removed outlier: 3.659A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 604 removed outlier: 4.097A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.660A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 4.011A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 710 through 715 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.748A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 762 removed outlier: 4.899A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 removed outlier: 3.908A pdb=" N GLU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 803 " --> pdb=" O LYS C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 835 through 861 removed outlier: 3.508A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 52 through 60 removed outlier: 4.218A pdb=" N LYS D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 120 removed outlier: 4.043A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 215 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.143A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.741A pdb=" N VAL D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 263 " --> pdb=" O SER D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.973A pdb=" N ASP D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.577A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 removed outlier: 3.511A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.311A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 523 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 removed outlier: 4.495A pdb=" N PHE D 550 " --> pdb=" O PRO D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 578 removed outlier: 4.642A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 614 removed outlier: 3.915A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 651 removed outlier: 3.505A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 656 removed outlier: 3.935A pdb=" N GLN D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 691 No H-bonds generated for 'chain 'D' and resid 689 through 691' Processing helix chain 'D' and resid 692 through 697 Processing helix chain 'D' and resid 700 through 707 removed outlier: 4.067A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 removed outlier: 3.511A pdb=" N THR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 784 removed outlier: 3.590A pdb=" N ASP D 777 " --> pdb=" O LYS D 773 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 818 through 844 removed outlier: 3.883A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 65 removed outlier: 3.796A pdb=" N GLN A 61 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 218 removed outlier: 5.973A pdb=" N ILE A 163 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 214 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 165 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 241 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 168 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 292 removed outlier: 4.049A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.354A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 538 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY A 778 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 538 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY A 778 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 777 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 511 Processing sheet with id=AA9, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.697A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 125 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.615A pdb=" N PHE B 169 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 202 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 171 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 173 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 172 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'B' and resid 417 through 420 Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 60 through 65 removed outlier: 3.796A pdb=" N GLN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 211 through 218 removed outlier: 5.973A pdb=" N ILE C 163 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C 214 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 165 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 241 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 168 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 291 through 292 removed outlier: 4.047A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.354A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 538 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY C 778 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 538 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY C 778 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 777 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 508 through 511 Processing sheet with id=AC8, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC9, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.696A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY D 125 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.615A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 172 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD3, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AD4, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 934 hydrogen bonds defined for protein. 2664 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: 4.43 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3670 1.31 - 1.44: 6017 1.44 - 1.57: 12767 1.57 - 1.70: 0 1.70 - 1.83: 214 Bond restraints: 22668 Sorted by residual: bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.455 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 22663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 30665 2.85 - 5.70: 349 5.70 - 8.55: 44 8.55 - 11.39: 2 11.39 - 14.24: 2 Bond angle restraints: 31062 Sorted by residual: angle pdb=" N GLN C 791 " pdb=" CA GLN C 791 " pdb=" C GLN C 791 " ideal model delta sigma weight residual 111.28 104.55 6.73 1.09e+00 8.42e-01 3.81e+01 angle pdb=" N GLN A 791 " pdb=" CA GLN A 791 " pdb=" C GLN A 791 " ideal model delta sigma weight residual 111.28 104.58 6.70 1.09e+00 8.42e-01 3.77e+01 angle pdb=" C ASP D 661 " pdb=" N GLN D 662 " pdb=" CA GLN D 662 " ideal model delta sigma weight residual 121.90 114.25 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C ASP B 661 " pdb=" N GLN B 662 " pdb=" CA GLN B 662 " ideal model delta sigma weight residual 121.90 114.26 7.64 1.26e+00 6.30e-01 3.68e+01 angle pdb=" O LYS C 790 " pdb=" C LYS C 790 " pdb=" N GLN C 791 " ideal model delta sigma weight residual 122.08 128.20 -6.12 1.07e+00 8.73e-01 3.27e+01 ... (remaining 31057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11932 17.72 - 35.45: 990 35.45 - 53.17: 176 53.17 - 70.90: 52 70.90 - 88.62: 12 Dihedral angle restraints: 13162 sinusoidal: 4208 harmonic: 8954 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 329 " pdb=" CB CYS C 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.94 62.06 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.95 62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 150.05 -57.05 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 13159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 3792 0.303 - 0.606: 2 0.606 - 0.909: 0 0.909 - 1.211: 0 1.211 - 1.514: 2 Chirality restraints: 3796 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 chirality pdb=" CG QGM A1001 " pdb=" CB QGM A1001 " pdb=" CD1 QGM A1001 " pdb=" ND2 QGM A1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 3793 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 792 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C GLN A 792 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 792 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 793 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 792 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN C 792 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN C 792 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 793 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 791 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C GLN A 791 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 791 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 792 " 0.012 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1107 2.70 - 3.25: 24779 3.25 - 3.80: 34053 3.80 - 4.35: 39907 4.35 - 4.90: 63555 Nonbonded interactions: 163401 Sorted by model distance: nonbonded pdb=" O ASP C 248 " pdb=" OG1 THR C 251 " model vdw 2.150 3.040 nonbonded pdb=" O ASP A 248 " pdb=" OG1 THR A 251 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASP C 450 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASP A 450 " model vdw 2.155 3.040 nonbonded pdb=" O LEU A 487 " pdb=" OG1 THR A 490 " model vdw 2.158 3.040 ... (remaining 163396 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.860 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 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 : 0.006 0.125 22694 Z= 0.283 Angle : 1.012 52.011 31116 Z= 0.514 Chirality : 0.059 1.514 3796 Planarity : 0.005 0.047 3930 Dihedral : 14.182 88.623 7316 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 1.71 % Allowed : 8.44 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.12 (0.12), residues: 3054 helix: -2.89 (0.12), residues: 1128 sheet: -3.46 (0.21), residues: 334 loop : -3.86 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 380 TYR 0.024 0.002 TYR A 128 PHE 0.015 0.002 PHE C 630 TRP 0.017 0.002 TRP A 789 HIS 0.007 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.28 (22668) covalent geometry : angle 0.83408 / 0.48 (31062) SS BOND : bond 0.00811 / 0.62 ( 18) SS BOND : angle 1.89578 / 1.74 ( 36) hydrogen bonds : bond 0.17478 / 12.35 ( 926) hydrogen bonds : angle 8.05952 / 5.73 ( 2664) Misc. bond : bond 0.00029 / 0.01 ( 2) link_BETA1-4 : bond 0.06470 / 3.25 ( 2) link_BETA1-4 : angle 40.97723 / 21.15 ( 6) link_NAG-ASN : bond 0.00406 / 0.20 ( 4) link_NAG-ASN : angle 1.68962 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6381 (tpp) cc_final: 0.5975 (tpt) REVERT: A 597 MET cc_start: 0.7153 (ttt) cc_final: 0.6548 (ttt) REVERT: B 366 LEU cc_start: 0.5064 (tp) cc_final: 0.4855 (tp) REVERT: B 426 SER cc_start: 0.4249 (OUTLIER) cc_final: 0.4007 (m) REVERT: C 154 MET cc_start: 0.5906 (tpp) cc_final: 0.4804 (tpt) REVERT: C 486 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8080 (tptp) REVERT: D 37 ILE cc_start: 0.6325 (mp) cc_final: 0.6001 (mt) REVERT: D 188 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7472 (t) REVERT: D 258 VAL cc_start: 0.6875 (m) cc_final: 0.6573 (m) REVERT: D 426 SER cc_start: 0.5455 (OUTLIER) cc_final: 0.4872 (m) REVERT: D 809 MET cc_start: 0.8685 (tmm) cc_final: 0.8421 (tmm) outliers start: 36 outliers final: 17 residues processed: 324 average time/residue: 0.1185 time to fit residues: 64.8261 Evaluate side-chains 234 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS A 73 GLN A 134 HIS A 146 HIS A 291 GLN A 371 GLN B 110 GLN B 159 ASN B 621 GLN C 38 HIS C 70 ASN C 73 GLN C 134 HIS C 146 HIS C 291 GLN C 371 GLN C 498 HIS C 542 ASN D 110 GLN D 621 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089187 restraints weight = 89166.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088509 restraints weight = 54028.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089293 restraints weight = 51475.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.089556 restraints weight = 40599.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089687 restraints weight = 38478.869| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22694 Z= 0.179 Angle : 0.714 8.791 31116 Z= 0.375 Chirality : 0.047 0.188 3796 Planarity : 0.005 0.041 3930 Dihedral : 6.630 54.534 3218 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.76 (0.13), residues: 3054 helix: -1.45 (0.14), residues: 1192 sheet: -3.05 (0.22), residues: 332 loop : -3.31 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 716 TYR 0.019 0.001 TYR C 128 PHE 0.022 0.002 PHE A 805 TRP 0.016 0.002 TRP A 789 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (22668) covalent geometry : angle 0.71258 / 0.37 (31062) SS BOND : bond 0.00460 / 0.33 ( 18) SS BOND : angle 1.40978 / 1.13 ( 36) hydrogen bonds : bond 0.04626 / 3.22 ( 926) hydrogen bonds : angle 6.36916 / 4.52 ( 2664) Misc. bond : bond 0.00087 / 0.04 ( 2) link_BETA1-4 : bond 0.00775 / 0.40 ( 2) link_BETA1-4 : angle 1.77598 / 0.94 ( 6) link_NAG-ASN : bond 0.00188 / 0.09 ( 4) link_NAG-ASN : angle 1.00963 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.696 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 486 LYS cc_start: 0.9417 (tmtt) cc_final: 0.9170 (ttpt) REVERT: A 720 LEU cc_start: 0.8755 (mt) cc_final: 0.8229 (mt) REVERT: B 561 MET cc_start: 0.9058 (ttm) cc_final: 0.8854 (ttm) REVERT: B 609 LEU cc_start: 0.9149 (mm) cc_final: 0.8916 (tt) REVERT: B 742 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7743 (tmm-80) REVERT: C 486 LYS cc_start: 0.9487 (tmtt) cc_final: 0.9279 (ttpt) REVERT: C 720 LEU cc_start: 0.8864 (mt) cc_final: 0.8351 (mt) REVERT: D 561 MET cc_start: 0.8992 (ttm) cc_final: 0.8542 (ttm) REVERT: D 742 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8173 (tmm-80) REVERT: D 809 MET cc_start: 0.8675 (tmm) cc_final: 0.8284 (tmm) outliers start: 2 outliers final: 0 residues processed: 299 average time/residue: 0.1118 time to fit residues: 57.5750 Evaluate side-chains 224 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 206 optimal weight: 0.2980 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 255 optimal weight: 20.0000 chunk 145 optimal weight: 0.4980 chunk 280 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS A 592 HIS B 672 GLN B 840 HIS C 38 HIS D 616 ASN D 672 GLN D 840 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.112951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094790 restraints weight = 89916.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095160 restraints weight = 54732.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095495 restraints weight = 58301.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.096075 restraints weight = 42112.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.096341 restraints weight = 37775.886| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22694 Z= 0.142 Angle : 0.651 8.429 31116 Z= 0.343 Chirality : 0.045 0.175 3796 Planarity : 0.004 0.051 3930 Dihedral : 6.234 54.442 3218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.01 (0.14), residues: 3054 helix: -0.62 (0.15), residues: 1188 sheet: -2.71 (0.24), residues: 348 loop : -3.04 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 693 TYR 0.019 0.001 TYR C 128 PHE 0.021 0.002 PHE B 144 TRP 0.014 0.001 TRP C 789 HIS 0.007 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22668) covalent geometry : angle 0.64920 / 0.34 (31062) SS BOND : bond 0.00940 / 0.68 ( 18) SS BOND : angle 1.23947 / 1.01 ( 36) hydrogen bonds : bond 0.04058 / 2.82 ( 926) hydrogen bonds : angle 5.84485 / 4.16 ( 2664) Misc. bond : bond 0.00041 / 0.02 ( 2) link_BETA1-4 : bond 0.00471 / 0.24 ( 2) link_BETA1-4 : angle 1.58805 / 0.90 ( 6) link_NAG-ASN : bond 0.00233 / 0.12 ( 4) link_NAG-ASN : angle 1.10542 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 MET cc_start: 0.9058 (ttm) cc_final: 0.8424 (ttm) REVERT: B 59 PHE cc_start: 0.7340 (m-80) cc_final: 0.7060 (m-80) REVERT: B 161 MET cc_start: 0.5245 (mtp) cc_final: 0.4712 (ttm) REVERT: B 285 TRP cc_start: 0.8040 (m100) cc_final: 0.7238 (m100) REVERT: B 561 MET cc_start: 0.9021 (ttm) cc_final: 0.8813 (ttm) REVERT: B 609 LEU cc_start: 0.9271 (mm) cc_final: 0.9067 (tt) REVERT: B 702 MET cc_start: 0.9128 (mtt) cc_final: 0.8704 (mtm) REVERT: B 742 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7790 (tmm-80) REVERT: B 829 MET cc_start: 0.8921 (mtp) cc_final: 0.8544 (mtp) REVERT: D 702 MET cc_start: 0.9020 (mtt) cc_final: 0.8564 (mtm) REVERT: D 742 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8197 (ttp80) REVERT: D 809 MET cc_start: 0.8567 (tmm) cc_final: 0.8304 (tmm) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1123 time to fit residues: 58.2118 Evaluate side-chains 227 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 6 optimal weight: 0.0010 chunk 7 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 305 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.112063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.092797 restraints weight = 86799.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093508 restraints weight = 49408.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093937 restraints weight = 39796.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094228 restraints weight = 34792.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.094652 restraints weight = 32213.640| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22694 Z= 0.118 Angle : 0.625 11.451 31116 Z= 0.327 Chirality : 0.045 0.169 3796 Planarity : 0.004 0.042 3930 Dihedral : 5.871 53.446 3218 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.15), residues: 3054 helix: -0.16 (0.15), residues: 1190 sheet: -2.36 (0.25), residues: 366 loop : -2.86 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 693 TYR 0.015 0.001 TYR A 128 PHE 0.025 0.001 PHE D 653 TRP 0.014 0.001 TRP B 610 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22668) covalent geometry : angle 0.62342 / 0.33 (31062) SS BOND : bond 0.00608 / 0.44 ( 18) SS BOND : angle 1.28201 / 1.12 ( 36) hydrogen bonds : bond 0.03629 / 2.52 ( 926) hydrogen bonds : angle 5.47977 / 3.91 ( 2664) Misc. bond : bond 0.00017 / 0.01 ( 2) link_BETA1-4 : bond 0.00440 / 0.22 ( 2) link_BETA1-4 : angle 1.56044 / 0.88 ( 6) link_NAG-ASN : bond 0.00233 / 0.12 ( 4) link_NAG-ASN : angle 0.96127 / 0.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8184 (tp30) cc_final: 0.7961 (tp30) REVERT: A 491 MET cc_start: 0.8581 (mtp) cc_final: 0.8091 (mtm) REVERT: A 597 MET cc_start: 0.9068 (ttm) cc_final: 0.8433 (ttm) REVERT: A 628 MET cc_start: 0.8469 (tpp) cc_final: 0.8135 (tpp) REVERT: A 652 ILE cc_start: 0.9194 (tp) cc_final: 0.8972 (tp) REVERT: B 59 PHE cc_start: 0.7379 (m-80) cc_final: 0.7003 (m-10) REVERT: B 285 TRP cc_start: 0.7892 (m100) cc_final: 0.7030 (m100) REVERT: B 561 MET cc_start: 0.8831 (ttm) cc_final: 0.8527 (ttm) REVERT: B 654 MET cc_start: 0.8329 (mtp) cc_final: 0.8125 (mtp) REVERT: B 742 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7568 (tmm-80) REVERT: B 829 MET cc_start: 0.8975 (mtp) cc_final: 0.8662 (mtp) REVERT: C 585 LEU cc_start: 0.8525 (mm) cc_final: 0.8303 (mm) REVERT: D 37 ILE cc_start: 0.6319 (mt) cc_final: 0.6106 (mp) REVERT: D 561 MET cc_start: 0.9032 (ttm) cc_final: 0.8626 (ttm) REVERT: D 702 MET cc_start: 0.8694 (mtt) cc_final: 0.8431 (mtm) REVERT: D 742 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8112 (ttp80) REVERT: D 809 MET cc_start: 0.8441 (tmm) cc_final: 0.8133 (tmm) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1138 time to fit residues: 61.8564 Evaluate side-chains 246 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 234 optimal weight: 0.0870 chunk 83 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 249 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS A 50 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.116020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096803 restraints weight = 87953.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.098354 restraints weight = 48209.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.098921 restraints weight = 36003.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.099180 restraints weight = 30807.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099293 restraints weight = 28718.564| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22694 Z= 0.107 Angle : 0.597 9.029 31116 Z= 0.309 Chirality : 0.044 0.174 3796 Planarity : 0.004 0.041 3930 Dihedral : 5.468 52.186 3218 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.13 (0.15), residues: 3054 helix: 0.19 (0.15), residues: 1194 sheet: -2.06 (0.25), residues: 370 loop : -2.68 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 693 TYR 0.023 0.001 TYR A 668 PHE 0.020 0.001 PHE D 653 TRP 0.017 0.001 TRP C 584 HIS 0.005 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (22668) covalent geometry : angle 0.59597 / 0.31 (31062) SS BOND : bond 0.00475 / 0.35 ( 18) SS BOND : angle 1.18031 / 0.93 ( 36) hydrogen bonds : bond 0.03259 / 2.28 ( 926) hydrogen bonds : angle 5.15464 / 3.68 ( 2664) Misc. bond : bond 0.00003 / 0.00 ( 2) link_BETA1-4 : bond 0.00691 / 0.35 ( 2) link_BETA1-4 : angle 1.55094 / 0.87 ( 6) link_NAG-ASN : bond 0.00386 / 0.20 ( 4) link_NAG-ASN : angle 0.85189 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7638 (tpt) cc_final: 0.7274 (tpp) REVERT: A 376 ASN cc_start: 0.8830 (t0) cc_final: 0.8586 (t0) REVERT: A 482 ASP cc_start: 0.8627 (m-30) cc_final: 0.8304 (t70) REVERT: A 491 MET cc_start: 0.8566 (mtp) cc_final: 0.7742 (mtm) REVERT: A 493 PHE cc_start: 0.7792 (m-10) cc_final: 0.7523 (m-10) REVERT: A 585 LEU cc_start: 0.8524 (mm) cc_final: 0.8025 (pp) REVERT: A 597 MET cc_start: 0.9137 (ttm) cc_final: 0.8478 (ttm) REVERT: B 59 PHE cc_start: 0.7466 (m-80) cc_final: 0.6843 (m-10) REVERT: B 561 MET cc_start: 0.8971 (ttm) cc_final: 0.8540 (ttm) REVERT: B 612 LEU cc_start: 0.8935 (tp) cc_final: 0.8726 (tt) REVERT: B 701 GLU cc_start: 0.8639 (mp0) cc_final: 0.8375 (mp0) REVERT: B 742 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7645 (tmm-80) REVERT: B 797 LEU cc_start: 0.8581 (mt) cc_final: 0.8239 (mp) REVERT: C 482 ASP cc_start: 0.8630 (m-30) cc_final: 0.8308 (t70) REVERT: C 597 MET cc_start: 0.9032 (ttt) cc_final: 0.8762 (ttm) REVERT: C 652 ILE cc_start: 0.9082 (tp) cc_final: 0.8876 (tp) REVERT: C 655 MET cc_start: 0.8038 (tpt) cc_final: 0.7836 (mmm) REVERT: C 723 MET cc_start: 0.5600 (mpp) cc_final: 0.5339 (mpp) REVERT: D 498 ILE cc_start: 0.9028 (mm) cc_final: 0.8821 (mm) REVERT: D 561 MET cc_start: 0.9009 (ttm) cc_final: 0.8455 (ttm) REVERT: D 565 MET cc_start: 0.8571 (mmm) cc_final: 0.8038 (mmm) REVERT: D 701 GLU cc_start: 0.8619 (mp0) cc_final: 0.8416 (pm20) REVERT: D 706 MET cc_start: 0.7068 (mpp) cc_final: 0.6859 (mtm) REVERT: D 809 MET cc_start: 0.8336 (tmm) cc_final: 0.8036 (tmm) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1153 time to fit residues: 67.0146 Evaluate side-chains 252 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 203 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 197 optimal weight: 0.0670 chunk 28 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS B 60 HIS B 153 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 HIS D 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.113698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.094979 restraints weight = 89873.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095813 restraints weight = 51891.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096138 restraints weight = 41528.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.096416 restraints weight = 36660.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.096640 restraints weight = 33881.279| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22694 Z= 0.142 Angle : 0.623 8.835 31116 Z= 0.324 Chirality : 0.044 0.200 3796 Planarity : 0.004 0.048 3930 Dihedral : 5.501 52.036 3218 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.06 (0.15), residues: 3054 helix: 0.24 (0.15), residues: 1190 sheet: -2.03 (0.26), residues: 366 loop : -2.61 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 774 TYR 0.019 0.001 TYR A 128 PHE 0.028 0.001 PHE D 653 TRP 0.019 0.001 TRP B 772 HIS 0.006 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (22668) covalent geometry : angle 0.62135 / 0.32 (31062) SS BOND : bond 0.00488 / 0.36 ( 18) SS BOND : angle 1.31331 / 1.05 ( 36) hydrogen bonds : bond 0.03470 / 2.41 ( 926) hydrogen bonds : angle 5.19989 / 3.72 ( 2664) Misc. bond : bond 0.00032 / 0.02 ( 2) link_BETA1-4 : bond 0.00817 / 0.42 ( 2) link_BETA1-4 : angle 1.56166 / 0.90 ( 6) link_NAG-ASN : bond 0.00271 / 0.14 ( 4) link_NAG-ASN : angle 0.97842 / 0.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.794 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: A 375 MET cc_start: 0.7911 (tpt) cc_final: 0.7594 (tpp) REVERT: A 491 MET cc_start: 0.8451 (mtp) cc_final: 0.7696 (mtm) REVERT: A 493 PHE cc_start: 0.7792 (m-10) cc_final: 0.7562 (m-10) REVERT: B 161 MET cc_start: 0.4973 (mtp) cc_final: 0.4447 (ttm) REVERT: B 285 TRP cc_start: 0.7778 (m100) cc_final: 0.7414 (m100) REVERT: B 561 MET cc_start: 0.8828 (ttm) cc_final: 0.8510 (ttm) REVERT: B 742 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7780 (tmm-80) REVERT: C 375 MET cc_start: 0.8122 (tpt) cc_final: 0.7690 (tpp) REVERT: C 376 ASN cc_start: 0.8420 (t0) cc_final: 0.8186 (t0) REVERT: D 233 THR cc_start: 0.6915 (p) cc_final: 0.6379 (t) REVERT: D 561 MET cc_start: 0.8951 (ttm) cc_final: 0.8440 (ttm) REVERT: D 701 GLU cc_start: 0.8584 (mp0) cc_final: 0.8376 (pm20) REVERT: D 706 MET cc_start: 0.6983 (mpp) cc_final: 0.6744 (mtm) REVERT: D 809 MET cc_start: 0.8409 (tmm) cc_final: 0.8093 (tmm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1135 time to fit residues: 60.8791 Evaluate side-chains 238 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 107 optimal weight: 40.0000 chunk 231 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094015 restraints weight = 89138.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.093492 restraints weight = 50353.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.094477 restraints weight = 45104.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094936 restraints weight = 35122.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.095063 restraints weight = 32857.453| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22694 Z= 0.178 Angle : 0.660 8.752 31116 Z= 0.344 Chirality : 0.045 0.157 3796 Planarity : 0.004 0.051 3930 Dihedral : 5.735 53.671 3218 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.10 (0.15), residues: 3054 helix: 0.16 (0.15), residues: 1190 sheet: -2.11 (0.25), residues: 380 loop : -2.57 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 742 TYR 0.021 0.001 TYR C 128 PHE 0.035 0.002 PHE D 653 TRP 0.024 0.002 TRP A 789 HIS 0.005 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (22668) covalent geometry : angle 0.65782 / 0.34 (31062) SS BOND : bond 0.00590 / 0.41 ( 18) SS BOND : angle 1.38333 / 1.14 ( 36) hydrogen bonds : bond 0.03784 / 2.60 ( 926) hydrogen bonds : angle 5.32738 / 3.81 ( 2664) Misc. bond : bond 0.00051 / 0.03 ( 2) link_BETA1-4 : bond 0.00911 / 0.48 ( 2) link_BETA1-4 : angle 1.67489 / 0.98 ( 6) link_NAG-ASN : bond 0.00336 / 0.17 ( 4) link_NAG-ASN : angle 1.16861 / 0.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.8048 (t70) cc_final: 0.7719 (t70) REVERT: A 652 ILE cc_start: 0.8997 (tp) cc_final: 0.8784 (tp) REVERT: B 503 MET cc_start: 0.8254 (mmt) cc_final: 0.8053 (mmm) REVERT: B 561 MET cc_start: 0.8990 (ttm) cc_final: 0.8532 (ttm) REVERT: B 742 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8049 (tmm-80) REVERT: C 375 MET cc_start: 0.8577 (tpt) cc_final: 0.8199 (tpp) REVERT: C 376 ASN cc_start: 0.8643 (t0) cc_final: 0.8399 (t0) REVERT: C 482 ASP cc_start: 0.7856 (t70) cc_final: 0.7532 (t70) REVERT: C 491 MET cc_start: 0.8418 (mtm) cc_final: 0.8111 (mpp) REVERT: C 493 PHE cc_start: 0.7264 (m-10) cc_final: 0.6980 (m-10) REVERT: C 723 MET cc_start: 0.6249 (mpp) cc_final: 0.5967 (mpp) REVERT: D 142 MET cc_start: 0.7208 (pmm) cc_final: 0.6339 (pmm) REVERT: D 233 THR cc_start: 0.6981 (p) cc_final: 0.6512 (t) REVERT: D 561 MET cc_start: 0.9083 (ttm) cc_final: 0.8492 (ttm) REVERT: D 701 GLU cc_start: 0.8740 (mp0) cc_final: 0.8442 (pm20) REVERT: D 809 MET cc_start: 0.8401 (tmm) cc_final: 0.8122 (tmm) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1100 time to fit residues: 58.7501 Evaluate side-chains 237 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 206 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 238 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 225 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS A 50 ASN ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.115236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096997 restraints weight = 87364.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097077 restraints weight = 57331.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097695 restraints weight = 45122.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097876 restraints weight = 40620.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098176 restraints weight = 37568.902| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22694 Z= 0.112 Angle : 0.614 8.411 31116 Z= 0.315 Chirality : 0.044 0.164 3796 Planarity : 0.004 0.048 3930 Dihedral : 5.402 52.455 3218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.85 (0.15), residues: 3054 helix: 0.44 (0.15), residues: 1180 sheet: -1.96 (0.26), residues: 366 loop : -2.48 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 380 TYR 0.017 0.001 TYR C 128 PHE 0.029 0.001 PHE A 575 TRP 0.021 0.001 TRP D 285 HIS 0.009 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (22668) covalent geometry : angle 0.61231 / 0.31 (31062) SS BOND : bond 0.00543 / 0.41 ( 18) SS BOND : angle 1.27038 / 1.00 ( 36) hydrogen bonds : bond 0.03395 / 2.37 ( 926) hydrogen bonds : angle 5.09917 / 3.64 ( 2664) Misc. bond : bond 0.00017 / 0.01 ( 2) link_BETA1-4 : bond 0.00905 / 0.44 ( 2) link_BETA1-4 : angle 1.66107 / 0.96 ( 6) link_NAG-ASN : bond 0.00310 / 0.16 ( 4) link_NAG-ASN : angle 0.89170 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7789 (tpt) cc_final: 0.7524 (tpp) REVERT: A 482 ASP cc_start: 0.7893 (t70) cc_final: 0.7602 (t70) REVERT: A 662 MET cc_start: 0.8963 (tmm) cc_final: 0.8685 (tmm) REVERT: B 161 MET cc_start: 0.4589 (mtp) cc_final: 0.4098 (ttm) REVERT: B 561 MET cc_start: 0.8936 (ttm) cc_final: 0.8493 (ttm) REVERT: C 375 MET cc_start: 0.8068 (tpt) cc_final: 0.7646 (tpp) REVERT: C 482 ASP cc_start: 0.7921 (t70) cc_final: 0.7566 (t70) REVERT: C 576 MET cc_start: 0.7093 (mmm) cc_final: 0.6863 (tpt) REVERT: C 597 MET cc_start: 0.9084 (ttt) cc_final: 0.8851 (ttm) REVERT: D 142 MET cc_start: 0.7210 (pmm) cc_final: 0.6438 (pmm) REVERT: D 233 THR cc_start: 0.6780 (p) cc_final: 0.6317 (t) REVERT: D 561 MET cc_start: 0.9043 (ttm) cc_final: 0.8443 (ttm) REVERT: D 701 GLU cc_start: 0.8625 (mp0) cc_final: 0.8402 (pm20) REVERT: D 809 MET cc_start: 0.8278 (tmm) cc_final: 0.8000 (tmm) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1097 time to fit residues: 59.2546 Evaluate side-chains 236 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 293 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 164 optimal weight: 0.0670 chunk 237 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096330 restraints weight = 88681.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.097166 restraints weight = 51332.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097534 restraints weight = 40834.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.097819 restraints weight = 36364.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.097985 restraints weight = 33505.699| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22694 Z= 0.126 Angle : 0.631 13.919 31116 Z= 0.325 Chirality : 0.044 0.160 3796 Planarity : 0.004 0.047 3930 Dihedral : 5.358 52.129 3218 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.76 (0.15), residues: 3054 helix: 0.49 (0.15), residues: 1180 sheet: -1.78 (0.27), residues: 356 loop : -2.46 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 489 TYR 0.017 0.001 TYR C 128 PHE 0.022 0.001 PHE A 575 TRP 0.021 0.001 TRP D 285 HIS 0.008 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22668) covalent geometry : angle 0.62993 / 0.32 (31062) SS BOND : bond 0.00423 / 0.30 ( 18) SS BOND : angle 1.18891 / 0.96 ( 36) hydrogen bonds : bond 0.03453 / 2.38 ( 926) hydrogen bonds : angle 5.07817 / 3.63 ( 2664) Misc. bond : bond 0.00033 / 0.02 ( 2) link_BETA1-4 : bond 0.00444 / 0.23 ( 2) link_BETA1-4 : angle 1.69694 / 0.98 ( 6) link_NAG-ASN : bond 0.00262 / 0.13 ( 4) link_NAG-ASN : angle 0.83560 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7891 (tpt) cc_final: 0.7674 (tpp) REVERT: A 482 ASP cc_start: 0.7721 (t70) cc_final: 0.7430 (t70) REVERT: B 561 MET cc_start: 0.8853 (ttm) cc_final: 0.8417 (ttm) REVERT: C 375 MET cc_start: 0.8191 (tpt) cc_final: 0.7875 (tpp) REVERT: C 482 ASP cc_start: 0.7822 (t70) cc_final: 0.7504 (t70) REVERT: C 576 MET cc_start: 0.6645 (mmm) cc_final: 0.6443 (tpt) REVERT: D 142 MET cc_start: 0.7085 (pmm) cc_final: 0.6376 (pmm) REVERT: D 233 THR cc_start: 0.6842 (p) cc_final: 0.6408 (t) REVERT: D 561 MET cc_start: 0.8942 (ttm) cc_final: 0.8373 (ttm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1098 time to fit residues: 58.4713 Evaluate side-chains 238 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 15 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 210 optimal weight: 0.0050 chunk 276 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.110736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.092413 restraints weight = 88551.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092562 restraints weight = 52573.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093020 restraints weight = 43973.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093597 restraints weight = 36575.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093696 restraints weight = 32756.610| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22694 Z= 0.115 Angle : 0.621 12.907 31116 Z= 0.319 Chirality : 0.044 0.164 3796 Planarity : 0.004 0.048 3930 Dihedral : 5.253 51.788 3218 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.65 (0.15), residues: 3054 helix: 0.57 (0.16), residues: 1176 sheet: -1.70 (0.26), residues: 372 loop : -2.38 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 371 TYR 0.024 0.001 TYR B 282 PHE 0.022 0.001 PHE A 575 TRP 0.018 0.001 TRP D 285 HIS 0.008 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (22668) covalent geometry : angle 0.61971 / 0.32 (31062) SS BOND : bond 0.00431 / 0.31 ( 18) SS BOND : angle 1.14671 / 0.94 ( 36) hydrogen bonds : bond 0.03323 / 2.30 ( 926) hydrogen bonds : angle 5.01847 / 3.58 ( 2664) Misc. bond : bond 0.00028 / 0.01 ( 2) link_BETA1-4 : bond 0.00564 / 0.28 ( 2) link_BETA1-4 : angle 1.66603 / 0.96 ( 6) link_NAG-ASN : bond 0.00265 / 0.14 ( 4) link_NAG-ASN : angle 0.80555 / 0.44 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.7950 (t70) cc_final: 0.7615 (t70) REVERT: B 561 MET cc_start: 0.8974 (ttm) cc_final: 0.8471 (ttm) REVERT: C 375 MET cc_start: 0.8030 (tpt) cc_final: 0.7733 (tpp) REVERT: C 482 ASP cc_start: 0.7911 (t70) cc_final: 0.7580 (t70) REVERT: C 723 MET cc_start: 0.5908 (mpp) cc_final: 0.5698 (mpp) REVERT: D 142 MET cc_start: 0.7061 (pmm) cc_final: 0.6383 (pmm) REVERT: D 233 THR cc_start: 0.6810 (p) cc_final: 0.6390 (t) REVERT: D 561 MET cc_start: 0.9069 (ttm) cc_final: 0.8563 (ttm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1163 time to fit residues: 62.8236 Evaluate side-chains 237 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 253 optimal weight: 20.0000 chunk 273 optimal weight: 0.0470 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 302 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.116003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097415 restraints weight = 89300.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098254 restraints weight = 50450.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.098672 restraints weight = 40234.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.098940 restraints weight = 35313.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099148 restraints weight = 32678.388| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22694 Z= 0.116 Angle : 0.616 12.532 31116 Z= 0.316 Chirality : 0.044 0.166 3796 Planarity : 0.004 0.054 3930 Dihedral : 5.182 51.323 3218 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.57 (0.15), residues: 3054 helix: 0.61 (0.16), residues: 1188 sheet: -1.60 (0.27), residues: 372 loop : -2.35 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.016 0.001 TYR C 128 PHE 0.020 0.001 PHE A 575 TRP 0.032 0.001 TRP D 285 HIS 0.012 0.001 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22668) covalent geometry : angle 0.61410 / 0.31 (31062) SS BOND : bond 0.00427 / 0.31 ( 18) SS BOND : angle 1.46581 / 1.19 ( 36) hydrogen bonds : bond 0.03318 / 2.28 ( 926) hydrogen bonds : angle 5.00336 / 3.59 ( 2664) Misc. bond : bond 0.00031 / 0.02 ( 2) link_BETA1-4 : bond 0.00414 / 0.21 ( 2) link_BETA1-4 : angle 1.70186 / 0.98 ( 6) link_NAG-ASN : bond 0.00282 / 0.14 ( 4) link_NAG-ASN : angle 0.82460 / 0.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.90 seconds wall clock time: 54 minutes 38.77 seconds (3278.77 seconds total)