Starting phenix.real_space_refine on Fri Jun 5 15:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299.map" model { file = "/net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obu_70299/06_2026/9obu_70299_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 13478 2.51 5 N 3670 2.21 5 O 3917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5131 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1174 Unresolved non-hydrogen angles: 1486 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'ASN:plan1': 21, 'ARG:plan': 28, 'HIS:plan': 10, 'GLU:plan': 30, 'GLN:plan1': 17, 'PHE:plan': 12, 'ASP:plan': 21, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 662 Chain: "B" Number of atoms: 5097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5097 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 312} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1162 Unresolved non-hydrogen angles: 1475 Unresolved non-hydrogen dihedrals: 977 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ASP:plan': 37, 'GLU:plan': 39, 'HIS:plan': 9, 'PHE:plan': 16, 'ARG:plan': 15, 'ASN:plan1': 11, 'GLN:plan1': 15, 'TYR:plan': 14, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 710 Chain: "C" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5513 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'ASN:plan1': 16, 'ARG:plan': 20, 'HIS:plan': 7, 'GLU:plan': 25, 'GLN:plan1': 12, 'PHE:plan': 7, 'ASP:plan': 18, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 464 Chain: "D" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5427 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 27, 'TRANS': 758} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 815 Unresolved non-hydrogen angles: 1028 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 29, 'GLU:plan': 33, 'HIS:plan': 7, 'PHE:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 11, 'GLN:plan1': 12, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 514 Time building chain proxies: 5.74, per 1000 atoms: 0.27 Number of scatterers: 21168 At special positions: 0 Unit cell: (146.376, 142.096, 181.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 3917 8.00 N 3670 7.00 C 13478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 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 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5894 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 33 sheets defined 44.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 4.209A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.617A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.982A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.701A pdb=" N LEU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.801A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 4.152A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 457 through 471 removed outlier: 4.026A pdb=" N LEU A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.546A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.794A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.543A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.571A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.960A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.802A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.517A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.614A pdb=" N GLU A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.724A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.597A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 838 removed outlier: 3.546A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.258A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.644A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.055A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.508A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.538A pdb=" N ILE B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.768A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.528A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.587A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.884A pdb=" N VAL B 417 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.628A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.650A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 522' Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.617A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.736A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 656 removed outlier: 3.689A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 639 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.641A pdb=" N GLN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 706 removed outlier: 3.808A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.639A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.852A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.531A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 797 removed outlier: 3.578A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.917A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.998A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.544A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.378A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.770A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.237A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.700A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.076A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.222A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 262 removed outlier: 4.261A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.577A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.588A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.106A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.683A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.510A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.649A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 4.134A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 3.573A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 removed outlier: 3.694A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 removed outlier: 3.801A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 707 removed outlier: 3.592A pdb=" N MET C 706 " --> pdb=" O MET C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.530A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 721 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 722 " --> pdb=" O ILE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 744 removed outlier: 4.404A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 739 " --> pdb=" O VAL C 735 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.624A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 814 through 838 removed outlier: 3.556A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.552A pdb=" N LYS D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.530A pdb=" N ILE D 82 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.449A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.540A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.532A pdb=" N ILE D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.963A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.764A pdb=" N LEU D 223 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.920A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.756A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.589A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.745A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.539A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.605A pdb=" N VAL D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.841A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.567A pdb=" N GLU D 552 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 577 removed outlier: 3.925A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 580 No H-bonds generated for 'chain 'D' and resid 578 through 580' Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.833A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.580A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.634A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.569A pdb=" N SER D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.521A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.653A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 796 removed outlier: 3.615A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 793 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 845 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.611A pdb=" N LEU A 91 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.372A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.549A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.541A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.733A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.170A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 70 removed outlier: 7.386A pdb=" N ARG B 67 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 39 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 41 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 7.145A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.653A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.506A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 439 through 440 removed outlier: 3.536A pdb=" N ILE B 440 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 451 " --> pdb=" O ILE B 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.663A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.635A pdb=" N ALA C 31 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.454A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.985A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 478 Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.578A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.010A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'D' and resid 70 through 72 removed outlier: 5.816A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.727A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.855A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY D 511 " --> pdb=" O ALA D 765 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA D 765 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.855A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY D 511 " --> pdb=" O ALA D 765 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA D 765 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 421 Processing sheet with id=AD5, first strand: chain 'D' and resid 439 through 440 removed outlier: 4.176A pdb=" N GLY D 451 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.667A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2754 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: 4.36 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7065 1.34 - 1.46: 4784 1.46 - 1.58: 9540 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 21561 Sorted by residual: bond pdb=" CB PRO D 415 " pdb=" CG PRO D 415 " ideal model delta sigma weight residual 1.492 1.416 0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB ILE D 530 " pdb=" CG2 ILE D 530 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB ASP A 690 " pdb=" CG ASP A 690 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CG1 ILE B 498 " pdb=" CD1 ILE B 498 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.11e+00 bond pdb=" CA PRO C 142 " pdb=" C PRO C 142 " ideal model delta sigma weight residual 1.517 1.524 -0.007 6.70e-03 2.23e+04 1.07e+00 ... (remaining 21556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 29022 1.53 - 3.07: 436 3.07 - 4.60: 59 4.60 - 6.14: 14 6.14 - 7.67: 2 Bond angle restraints: 29533 Sorted by residual: angle pdb=" N VAL B 522 " pdb=" CA VAL B 522 " pdb=" C VAL B 522 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.12e+01 angle pdb=" N ASP B 77 " pdb=" CA ASP B 77 " pdb=" C ASP B 77 " ideal model delta sigma weight residual 108.07 110.43 -2.36 8.90e-01 1.26e+00 7.03e+00 angle pdb=" CA GLY C 537 " pdb=" C GLY C 537 " pdb=" N LEU C 538 " ideal model delta sigma weight residual 115.03 118.13 -3.10 1.27e+00 6.20e-01 5.96e+00 angle pdb=" N LYS B 504 " pdb=" CA LYS B 504 " pdb=" CB LYS B 504 " ideal model delta sigma weight residual 113.65 110.40 3.25 1.47e+00 4.63e-01 4.88e+00 angle pdb=" CA LEU C 736 " pdb=" CB LEU C 736 " pdb=" CG LEU C 736 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.81e+00 ... (remaining 29528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12144 17.48 - 34.96: 437 34.96 - 52.45: 55 52.45 - 69.93: 5 69.93 - 87.41: 4 Dihedral angle restraints: 12645 sinusoidal: 3536 harmonic: 9109 Sorted by residual: dihedral pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" N PRO B 680 " pdb=" CA PRO B 680 " ideal model delta harmonic sigma weight residual 180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU D 413 " pdb=" C GLU D 413 " pdb=" N ALA D 414 " pdb=" CA ALA D 414 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO D 679 " pdb=" C PRO D 679 " pdb=" N PRO D 680 " pdb=" CA PRO D 680 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 12642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2202 0.034 - 0.067: 977 0.067 - 0.101: 243 0.101 - 0.134: 151 0.134 - 0.168: 8 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA PHE C 753 " pdb=" N PHE C 753 " pdb=" C PHE C 753 " pdb=" CB PHE C 753 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL B 527 " pdb=" N VAL B 527 " pdb=" C VAL B 527 " pdb=" CB VAL B 527 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 3578 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 553 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 533 " 0.011 2.00e-02 2.50e+03 1.26e-02 2.80e+00 pdb=" CG PHE A 533 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 533 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 533 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 533 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 533 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 533 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 415 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.021 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2309 2.75 - 3.28: 20135 3.28 - 3.82: 31642 3.82 - 4.36: 35334 4.36 - 4.90: 64142 Nonbonded interactions: 153562 Sorted by model distance: nonbonded pdb=" O ILE A 664 " pdb=" OG1 THR A 749 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR D 167 " pdb=" OG1 THR D 428 " model vdw 2.210 3.040 nonbonded pdb=" O VAL B 501 " pdb=" NE2 GLN B 767 " model vdw 2.217 3.120 nonbonded pdb=" O THR C 302 " pdb=" OG1 THR C 317 " model vdw 2.223 3.040 nonbonded pdb=" O ALA B 794 " pdb=" OG1 THR B 798 " model vdw 2.228 3.040 ... (remaining 153557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 349 or (resid 350 through 351 and (name N or na \ me CA or name C or name O or name CB )) or resid 352 through 367 or (resid 368 a \ nd (name N or name CA or name C or name O or name CB )) or resid 369 through 474 \ or (resid 475 and (name N or name CA or name C or name O or name CB )) or resid \ 476 through 527 or (resid 528 and (name N or name CA or name C or name O or nam \ e CB )) or resid 529 through 551 or (resid 552 and (name N or name CA or name C \ or name O or name CB )) or resid 553 through 560 or (resid 561 and (name N or na \ me CA or name C or name O or name CB )) or resid 562 through 564 or (resid 565 a \ nd (name N or name CA or name C or name O or name CB )) or resid 566 through 603 \ or (resid 604 and (name N or name CA or name C or name O or name CB )) or resid \ 605 through 627 or (resid 628 through 629 and (name N or name CA or name C or n \ ame O or name CB )) or resid 630 through 724 or (resid 725 and (name N or name C \ A or name C or name O or name CB )) or resid 726 through 804 or (resid 805 throu \ gh 806 and (name N or name CA or name C or name O or name CB )) or resid 807 thr \ ough 819 or (resid 820 through 821 and (name N or name CA or name C or name O or \ name CB )) or resid 822 through 838)) selection = (chain 'C' and ((resid 25 through 29 and (name N or name CA or name C or name O \ or name CB )) or (resid 30 through 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 or (resid 113 through 119 and (name N or name CA or \ name C or name O or name CB )) or (resid 120 through 142 and (name N or name CA \ or name C or name O or name CB )) or resid 143 or (resid 144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 145 or (resid 146 through 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 through 149 \ or (resid 150 and (name N or name CA or name C or name O or name CB )) or resid \ 151 through 153 or (resid 154 through 156 and (name N or name CA or name C or na \ me O or name CB )) or resid 157 through 158 or (resid 159 and (name N or name CA \ or name C or name O or name CB )) or resid 160 or (resid 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 169 or (resid 170 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 181 and (name N or name CA or name C or name O or name CB \ )) or resid 182 or (resid 183 through 188 and (name N or name CA or name C or na \ me O or name CB )) or resid 189 or (resid 190 through 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 or (resid 195 through 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 200 or ( \ resid 201 through 203 and (name N or name CA or name C or name O or name CB )) o \ r resid 204 or (resid 205 through 209 and (name N or name CA or name C or name O \ or name CB )) or resid 210 through 211 or (resid 212 through 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 through 223 or (resid 22 \ 4 through 229 and (name N or name CA or name C or name O or name CB )) or resid \ 230 or (resid 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 or (resid 233 through 240 and (name N or name CA or name C or name O or \ name CB )) or resid 241 through 250 or (resid 251 through 255 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 256 through 262 and (name N or \ name CA or name C or name O or name CB )) or resid 263 or (resid 264 and (name N \ or name CA or name C or name O or name CB )) or resid 265 or (resid 266 and (na \ me N or name CA or name C or name O or name CB )) or resid 267 through 269 or (r \ esid 270 through 273 and (name N or name CA or name C or name O or name CB )) or \ (resid 274 through 285 and (name N or name CA or name C or name O or name CB )) \ or (resid 286 through 306 and (name N or name CA or name C or name O or name CB \ )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 310 through 317 and (name N or name CA or name C o \ r name O or name CB )) or resid 318 or (resid 319 through 332 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 333 through 335 and (name N or \ name CA or name C or name O or name CB )) or (resid 336 through 343 and (name N \ or name CA or name C or name O or name CB )) or (resid 344 through 351 and (name \ N or name CA or name C or name O or name CB )) or resid 352 or (resid 353 throu \ gh 354 and (name N or name CA or name C or name O or name CB )) or resid 355 or \ (resid 356 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 362 or (resid 363 and (name N or name CA or name C or name \ O or name CB )) or resid 364 through 365 or (resid 366 through 368 and (name N o \ r name CA or name C or name O or name CB )) or resid 369 through 372 or (resid 3 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 374 through \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) or r \ esid 380 through 385 or (resid 386 through 388 and (name N or name CA or name C \ or name O or name CB )) or resid 389 through 488 or (resid 489 and (name N or na \ me CA or name C or name O or name CB )) or resid 490 through 554 or (resid 555 t \ hrough 556 and (name N or name CA or name C or name O or name CB )) or resid 557 \ through 576 or (resid 577 through 584 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 624 or (resid 625 and (name N or name CA or \ name C or name O or name CB )) or resid 626 through 656 or (resid 657 through 6 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 663 through \ 750 or (resid 751 and (name N or name CA or name C or name O or name CB )) or r \ esid 752 through 795 or (resid 796 through 797 and (name N or name CA or name C \ or name O or name CB )) or resid 798 through 809 or (resid 810 through 812 and ( \ name N or name CA or name C or name O or name CB )) or resid 813 through 816 or \ (resid 817 through 821 and (name N or name CA or name C or name O or name CB )) \ or resid 822 through 838)) } ncs_group { reference = (chain 'B' and (resid 34 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 118 or (resid 119 through 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 or (resid 1 \ 26 through 127 and (name N or name CA or name C or name O or name CB )) or resid \ 128 through 169 or (resid 170 and (name N or name CA or name C or name O or nam \ e CB )) or resid 171 through 206 or (resid 207 through 211 and (name N or name C \ A or name C or name O or name CB )) or (resid 212 through 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 384 \ or (resid 385 through 390 and (name N or name CA or name C or name O or name CB \ )) or resid 391 through 393 or resid 403 through 469 or (resid 470 and (name N o \ r name CA or name C or name O or name CB )) or resid 471 through 490 or (resid 4 \ 91 and (name N or name CA or name C or name O or name CB )) or resid 492 through \ 540 or (resid 541 through 542 and (name N or name CA or name C or name O or nam \ e CB )) or resid 543 through 629 or (resid 630 through 631 and (name N or name C \ A or name C or name O or name CB )) or resid 632 through 677 or (resid 678 and ( \ name N or name CA or name C or name O or name CB )) or resid 679 through 700 or \ (resid 701 and (name N or name CA or name C or name O or name CB )) or resid 702 \ through 724 or (resid 725 and (name N or name CA or name C or name O or name CB \ )) or resid 726 through 823 or (resid 824 and (name N or name CA or name C or n \ ame O or name CB )) or resid 825 through 845)) selection = (chain 'D' and ((resid 34 through 42 and (name N or name CA or name C or name O \ or name CB )) or (resid 43 through 95 and (name N or name CA or name C or name O \ or name CB )) or resid 96 or (resid 97 through 102 and (name N or name CA or na \ me C or name O or name CB )) or resid 103 through 111 or (resid 112 through 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 12 \ 1 or (resid 122 through 124 and (name N or name CA or name C or name O or name C \ B )) or (resid 125 through 127 and (name N or name CA or name C or name O or nam \ e CB )) or resid 128 through 129 or (resid 130 through 140 and (name N or name C \ A or name C or name O or name CB )) or resid 141 or (resid 142 through 144 and ( \ name N or name CA or name C or name O or name CB )) or resid 145 or (resid 146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 147 through 151 \ or (resid 152 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or n \ ame O or name CB )) or resid 159 through 161 or (resid 162 through 163 and (name \ N or name CA or name C or name O or name CB )) or resid 164 or (resid 165 and ( \ name N or name CA or name C or name O or name CB )) or resid 166 through 183 or \ (resid 184 through 185 and (name N or name CA or name C or name O or name CB )) \ or resid 186 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 190 or (resid 191 and (name N or name CA or \ name C or name O or name CB )) or resid 192 or (resid 193 through 194 and (name \ N or name CA or name C or name O or name CB )) or resid 195 through 199 or (res \ id 200 through 201 and (name N or name CA or name C or name O or name CB )) or r \ esid 202 through 233 or (resid 234 through 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 through 260 or (resid 261 and (name N or na \ me CA or name C or name O or name CB )) or resid 262 through 267 or (resid 268 a \ nd (name N or name CA or name C or name O or name CB )) or resid 269 through 270 \ or (resid 271 through 272 and (name N or name CA or name C or name O or name CB \ )) or resid 273 through 280 or (resid 281 through 287 and (name N or name CA or \ name C or name O or name CB )) or (resid 288 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 or (resid 297 through 345 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 346 through 351 and \ (name N or name CA or name C or name O or name CB )) or resid 352 through 355 o \ r (resid 356 through 359 and (name N or name CA or name C or name O or name CB ) \ ) or resid 360 through 370 or (resid 371 through 375 and (name N or name CA or n \ ame C or name O or name CB )) or resid 376 through 377 or (resid 378 through 382 \ and (name N or name CA or name C or name O or name CB )) or resid 383 or (resid \ 384 through 390 and (name N or name CA or name C or name O or name CB )) or res \ id 391 through 422 or (resid 423 and (name N or name CA or name C or name O or n \ ame CB )) or resid 424 through 425 or (resid 426 and (name N or name CA or name \ C or name O or name CB )) or resid 427 through 430 or (resid 431 and (name N or \ name CA or name C or name O or name CB )) or resid 432 through 438 or (resid 439 \ through 450 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 51 or (resid 452 and (name N or name CA or name C or name O or name CB )) or res \ id 453 through 502 or (resid 503 and (name N or name CA or name C or name O or n \ ame CB )) or resid 504 through 530 or (resid 531 and (name N or name CA or name \ C or name O or name CB )) or resid 532 through 550 or (resid 551 through 552 and \ (name N or name CA or name C or name O or name CB )) or resid 553 through 559 o \ r (resid 560 through 561 and (name N or name CA or name C or name O or name CB ) \ ) or resid 562 through 565 or (resid 566 through 579 and (name N or name CA or n \ ame C or name O or name CB )) or resid 599 or (resid 600 through 602 and (name N \ or name CA or name C or name O or name CB )) or resid 603 or (resid 604 through \ 606 and (name N or name CA or name C or name O or name CB )) or resid 607 throu \ gh 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) or \ resid 663 through 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB )) or resid 671 through 714 or (resid 715 and (name N or name CA or n \ ame C or name O or name CB )) or resid 716 through 726 or (resid 727 through 728 \ and (name N or name CA or name C or name O or name CB )) or resid 729 through 7 \ 73 or (resid 774 and (name N or name CA or name C or name O or name CB )) or res \ id 775 through 789 or (resid 790 through 791 and (name N or name CA or name C or \ name O or name CB )) or resid 792 through 807 or (resid 808 through 810 and (na \ me N or name CA or name C or name O or name CB )) or resid 811 through 845)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.610 Find NCS groups from input model: 0.630 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: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.004 0.076 21575 Z= 0.169 Angle : 0.498 7.675 29561 Z= 0.274 Chirality : 0.043 0.168 3581 Planarity : 0.003 0.046 3828 Dihedral : 9.498 87.412 6709 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 0.36 % Allowed : 5.37 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.02 (0.15), residues: 3131 helix: 0.08 (0.15), residues: 1205 sheet: -0.67 (0.29), residues: 388 loop : -1.25 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.022 0.001 TYR D 479 PHE 0.029 0.002 PHE A 533 TRP 0.014 0.001 TRP A 768 HIS 0.008 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (21561) covalent geometry : angle 0.49792 / 0.27 (29533) SS BOND : bond 0.00280 / 0.24 ( 14) SS BOND : angle 0.85126 / 0.64 ( 28) hydrogen bonds : bond 0.29408 / 21.57 ( 946) hydrogen bonds : angle 7.74556 / 5.88 ( 2754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 403 time to evaluate : 0.816 Fit side-chains REVERT: A 415 MET cc_start: 0.7895 (ppp) cc_final: 0.7441 (ptt) REVERT: B 404 ASP cc_start: 0.6889 (m-30) cc_final: 0.6428 (p0) REVERT: B 824 MET cc_start: 0.7233 (mmt) cc_final: 0.6946 (mmt) outliers start: 6 outliers final: 2 residues processed: 407 average time/residue: 0.1333 time to fit residues: 88.2851 Evaluate side-chains 337 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 536 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 711 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS C 427 ASN C 525 GLN C 727 HIS C 770 GLN D 219 GLN D 672 GLN D 767 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.223236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.204381 restraints weight = 24418.316| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 0.95 r_work: 0.4018 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3896 rms_B_bonded: 3.16 restraints_weight: 0.1250 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21575 Z= 0.123 Angle : 0.502 7.241 29561 Z= 0.277 Chirality : 0.043 0.159 3581 Planarity : 0.004 0.050 3828 Dihedral : 4.124 58.283 3282 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 10.49 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3131 helix: 0.54 (0.14), residues: 1280 sheet: -0.62 (0.28), residues: 393 loop : -1.27 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 712 TYR 0.013 0.001 TYR B 479 PHE 0.023 0.002 PHE D 550 TRP 0.014 0.001 TRP B 607 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21561) covalent geometry : angle 0.50007 / 0.28 (29533) SS BOND : bond 0.00230 / 0.18 ( 14) SS BOND : angle 1.50494 / 1.11 ( 28) hydrogen bonds : bond 0.05512 / 4.01 ( 946) hydrogen bonds : angle 5.03495 / 3.81 ( 2754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 368 time to evaluate : 0.780 Fit side-chains REVERT: A 415 MET cc_start: 0.7965 (ppp) cc_final: 0.7497 (ptt) REVERT: B 782 GLN cc_start: 0.8164 (pt0) cc_final: 0.7899 (pt0) REVERT: D 368 ASN cc_start: 0.7588 (p0) cc_final: 0.7387 (p0) REVERT: D 706 MET cc_start: 0.8507 (mtm) cc_final: 0.8303 (mtm) outliers start: 28 outliers final: 14 residues processed: 382 average time/residue: 0.1306 time to fit residues: 81.7189 Evaluate side-chains 335 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 321 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 121 optimal weight: 0.9990 chunk 291 optimal weight: 0.0270 chunk 205 optimal weight: 0.8980 chunk 27 optimal weight: 30.0000 chunk 0 optimal weight: 80.0000 chunk 2 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 195 optimal weight: 0.1980 chunk 277 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 368 ASN B 649 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 571 HIS D 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.223829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206988 restraints weight = 24597.170| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 0.88 r_work: 0.4063 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.3964 rms_B_bonded: 2.71 restraints_weight: 0.1250 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21575 Z= 0.104 Angle : 0.463 10.934 29561 Z= 0.249 Chirality : 0.042 0.141 3581 Planarity : 0.003 0.055 3828 Dihedral : 3.898 56.787 3280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 1.97 % Allowed : 12.58 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3131 helix: 0.96 (0.15), residues: 1295 sheet: -0.49 (0.28), residues: 399 loop : -1.29 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 682 TYR 0.014 0.001 TYR B 254 PHE 0.029 0.001 PHE D 677 TRP 0.017 0.001 TRP B 607 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (21561) covalent geometry : angle 0.46243 / 0.25 (29533) SS BOND : bond 0.00247 / 0.19 ( 14) SS BOND : angle 1.10077 / 0.83 ( 28) hydrogen bonds : bond 0.04314 / 3.16 ( 946) hydrogen bonds : angle 4.36973 / 3.30 ( 2754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 337 time to evaluate : 0.831 Fit side-chains REVERT: A 415 MET cc_start: 0.7905 (ppp) cc_final: 0.7362 (ptt) REVERT: B 404 ASP cc_start: 0.6146 (p0) cc_final: 0.5882 (p0) outliers start: 33 outliers final: 18 residues processed: 352 average time/residue: 0.1253 time to fit residues: 73.5181 Evaluate side-chains 347 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 329 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 61 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 258 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.220182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.204474 restraints weight = 24359.693| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 0.81 r_work: 0.4017 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.3941 rms_B_bonded: 2.11 restraints_weight: 0.1250 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21575 Z= 0.198 Angle : 0.544 7.405 29561 Z= 0.294 Chirality : 0.045 0.186 3581 Planarity : 0.004 0.047 3828 Dihedral : 4.275 54.198 3280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 2.50 % Allowed : 13.42 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3131 helix: 0.94 (0.15), residues: 1290 sheet: -0.44 (0.28), residues: 372 loop : -1.39 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 712 TYR 0.022 0.001 TYR D 479 PHE 0.036 0.002 PHE A 533 TRP 0.016 0.001 TRP B 607 HIS 0.008 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (21561) covalent geometry : angle 0.54254 / 0.29 (29533) SS BOND : bond 0.00369 / 0.28 ( 14) SS BOND : angle 1.35599 / 1.03 ( 28) hydrogen bonds : bond 0.04935 / 3.58 ( 946) hydrogen bonds : angle 4.36241 / 3.31 ( 2754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 0.780 Fit side-chains REVERT: A 415 MET cc_start: 0.7942 (ppp) cc_final: 0.7427 (ptt) REVERT: A 665 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7057 (p) REVERT: B 404 ASP cc_start: 0.6348 (p0) cc_final: 0.6065 (p0) REVERT: C 789 ASP cc_start: 0.8235 (t0) cc_final: 0.7967 (t70) outliers start: 42 outliers final: 25 residues processed: 357 average time/residue: 0.1243 time to fit residues: 73.9874 Evaluate side-chains 347 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 321 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 23 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 192 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 152 optimal weight: 0.0060 chunk 187 optimal weight: 50.0000 chunk 51 optimal weight: 0.3980 chunk 189 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 440 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.223203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.206195 restraints weight = 24313.056| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 0.88 r_work: 0.4063 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.3949 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21575 Z= 0.096 Angle : 0.451 7.284 29561 Z= 0.243 Chirality : 0.042 0.143 3581 Planarity : 0.003 0.056 3828 Dihedral : 3.946 52.980 3280 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 1.91 % Allowed : 14.67 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3131 helix: 1.16 (0.15), residues: 1295 sheet: -0.47 (0.28), residues: 392 loop : -1.31 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.015 0.001 TYR B 179 PHE 0.019 0.001 PHE C 152 TRP 0.014 0.001 TRP B 607 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (21561) covalent geometry : angle 0.45024 / 0.24 (29533) SS BOND : bond 0.00186 / 0.15 ( 14) SS BOND : angle 0.95924 / 0.70 ( 28) hydrogen bonds : bond 0.03572 / 2.61 ( 946) hydrogen bonds : angle 4.06018 / 3.07 ( 2754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 330 time to evaluate : 0.755 Fit side-chains REVERT: B 404 ASP cc_start: 0.6398 (p0) cc_final: 0.6118 (p0) REVERT: D 706 MET cc_start: 0.8437 (mtm) cc_final: 0.8159 (mtm) outliers start: 32 outliers final: 22 residues processed: 349 average time/residue: 0.1226 time to fit residues: 71.5639 Evaluate side-chains 347 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 202 optimal weight: 0.0770 chunk 119 optimal weight: 20.0000 chunk 200 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 40.0000 chunk 131 optimal weight: 40.0000 chunk 180 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.222048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206809 restraints weight = 24286.059| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 0.78 r_work: 0.4067 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3992 rms_B_bonded: 2.15 restraints_weight: 0.1250 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21575 Z= 0.128 Angle : 0.476 6.992 29561 Z= 0.256 Chirality : 0.043 0.159 3581 Planarity : 0.003 0.055 3828 Dihedral : 3.990 52.116 3280 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 2.27 % Allowed : 14.49 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3131 helix: 1.23 (0.15), residues: 1290 sheet: -0.40 (0.28), residues: 378 loop : -1.31 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 505 TYR 0.017 0.001 TYR D 479 PHE 0.029 0.002 PHE A 533 TRP 0.013 0.001 TRP B 607 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (21561) covalent geometry : angle 0.47510 / 0.26 (29533) SS BOND : bond 0.00299 / 0.23 ( 14) SS BOND : angle 1.15419 / 0.84 ( 28) hydrogen bonds : bond 0.03797 / 2.76 ( 946) hydrogen bonds : angle 4.01458 / 3.04 ( 2754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 0.841 Fit side-chains REVERT: A 501 MET cc_start: 0.9001 (mtm) cc_final: 0.8799 (mtm) REVERT: B 404 ASP cc_start: 0.6420 (p0) cc_final: 0.6148 (p0) outliers start: 38 outliers final: 33 residues processed: 348 average time/residue: 0.1265 time to fit residues: 73.5979 Evaluate side-chains 355 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 753 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 137 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 50.0000 chunk 194 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 30 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.223415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.209725 restraints weight = 24364.220| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 0.72 r_work: 0.4142 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.4022 rms_B_bonded: 3.03 restraints_weight: 0.1250 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21575 Z= 0.099 Angle : 0.447 7.212 29561 Z= 0.241 Chirality : 0.042 0.141 3581 Planarity : 0.003 0.058 3828 Dihedral : 3.847 50.975 3280 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 2.50 % Allowed : 14.67 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3131 helix: 1.36 (0.15), residues: 1294 sheet: -0.42 (0.28), residues: 394 loop : -1.25 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 505 TYR 0.016 0.001 TYR B 179 PHE 0.023 0.001 PHE C 152 TRP 0.012 0.001 TRP B 607 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (21561) covalent geometry : angle 0.44578 / 0.24 (29533) SS BOND : bond 0.00192 / 0.15 ( 14) SS BOND : angle 0.94530 / 0.68 ( 28) hydrogen bonds : bond 0.03295 / 2.41 ( 946) hydrogen bonds : angle 3.86675 / 2.93 ( 2754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 0.804 Fit side-chains REVERT: B 404 ASP cc_start: 0.6377 (p0) cc_final: 0.6123 (p0) outliers start: 42 outliers final: 36 residues processed: 356 average time/residue: 0.1253 time to fit residues: 74.3609 Evaluate side-chains 365 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 121 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 4 optimal weight: 30.0000 chunk 105 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.223587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.209939 restraints weight = 24201.583| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 0.71 r_work: 0.4157 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work: 0.4070 rms_B_bonded: 2.42 restraints_weight: 0.1250 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21575 Z= 0.099 Angle : 0.450 7.649 29561 Z= 0.241 Chirality : 0.042 0.212 3581 Planarity : 0.003 0.060 3828 Dihedral : 3.803 50.299 3280 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.39 % Allowed : 15.21 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 3131 helix: 1.43 (0.15), residues: 1292 sheet: -0.39 (0.28), residues: 394 loop : -1.25 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 712 TYR 0.017 0.001 TYR B 179 PHE 0.030 0.001 PHE C 152 TRP 0.014 0.001 TRP B 607 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (21561) covalent geometry : angle 0.44938 / 0.24 (29533) SS BOND : bond 0.00193 / 0.14 ( 14) SS BOND : angle 1.05897 / 0.73 ( 28) hydrogen bonds : bond 0.03215 / 2.35 ( 946) hydrogen bonds : angle 3.80212 / 2.88 ( 2754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 0.805 Fit side-chains REVERT: B 404 ASP cc_start: 0.6397 (p0) cc_final: 0.6144 (p0) outliers start: 40 outliers final: 36 residues processed: 354 average time/residue: 0.1240 time to fit residues: 72.9401 Evaluate side-chains 360 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 56 optimal weight: 0.1980 chunk 284 optimal weight: 0.7980 chunk 308 optimal weight: 0.6980 chunk 304 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 219 optimal weight: 0.4980 chunk 213 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 767 GLN B 812 GLN C 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.224588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.211182 restraints weight = 24346.753| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 0.71 r_work: 0.4154 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.4048 rms_B_bonded: 2.69 restraints_weight: 0.1250 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21575 Z= 0.092 Angle : 0.441 7.610 29561 Z= 0.236 Chirality : 0.042 0.140 3581 Planarity : 0.003 0.060 3828 Dihedral : 3.720 49.545 3280 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.39 % Allowed : 15.32 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 3131 helix: 1.51 (0.15), residues: 1296 sheet: -0.32 (0.28), residues: 394 loop : -1.23 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 505 TYR 0.017 0.001 TYR B 179 PHE 0.029 0.001 PHE C 152 TRP 0.015 0.001 TRP B 607 HIS 0.004 0.000 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (21561) covalent geometry : angle 0.44090 / 0.24 (29533) SS BOND : bond 0.00152 / 0.12 ( 14) SS BOND : angle 0.85519 / 0.61 ( 28) hydrogen bonds : bond 0.02987 / 2.19 ( 946) hydrogen bonds : angle 3.73169 / 2.82 ( 2754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.827 Fit side-chains REVERT: B 404 ASP cc_start: 0.6401 (p0) cc_final: 0.6152 (p0) REVERT: C 780 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.7744 (m170) outliers start: 40 outliers final: 35 residues processed: 350 average time/residue: 0.1198 time to fit residues: 70.2556 Evaluate side-chains 359 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 290 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 171 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS D 698 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.217991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201257 restraints weight = 24380.921| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 0.87 r_work: 0.3959 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work: 0.3862 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 21575 Z= 0.347 Angle : 0.684 9.897 29561 Z= 0.368 Chirality : 0.051 0.240 3581 Planarity : 0.005 0.055 3828 Dihedral : 4.631 50.363 3280 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 2.33 % Allowed : 15.92 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3131 helix: 0.91 (0.15), residues: 1291 sheet: -0.56 (0.28), residues: 376 loop : -1.44 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 519 TYR 0.035 0.002 TYR D 479 PHE 0.044 0.003 PHE A 458 TRP 0.017 0.002 TRP B 607 HIS 0.011 0.002 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.35 (21561) covalent geometry : angle 0.68212 / 0.37 (29533) SS BOND : bond 0.00666 / 0.50 ( 14) SS BOND : angle 1.95526 / 1.38 ( 28) hydrogen bonds : bond 0.05556 / 4.00 ( 946) hydrogen bonds : angle 4.29464 / 3.26 ( 2754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.794 Fit side-chains REVERT: A 415 MET cc_start: 0.8059 (ppp) cc_final: 0.7667 (ptt) REVERT: A 665 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7182 (p) REVERT: B 385 GLN cc_start: 0.5716 (mp10) cc_final: 0.5046 (mp10) REVERT: B 404 ASP cc_start: 0.6591 (p0) cc_final: 0.6305 (p0) outliers start: 39 outliers final: 31 residues processed: 348 average time/residue: 0.1245 time to fit residues: 72.1704 Evaluate side-chains 354 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 753 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 214 optimal weight: 0.0170 chunk 75 optimal weight: 0.0270 chunk 253 optimal weight: 0.0050 chunk 269 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 616 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN C 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.218853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202209 restraints weight = 24283.678| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 0.86 r_work: 0.4004 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.3919 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 21575 Z= 0.236 Angle : 0.802 59.181 29561 Z= 0.453 Chirality : 0.048 0.652 3581 Planarity : 0.005 0.099 3828 Dihedral : 4.648 50.155 3280 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.29 % Favored : 93.61 % Rotamer: Outliers : 1.91 % Allowed : 16.76 % Favored : 81.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3131 helix: 0.91 (0.15), residues: 1291 sheet: -0.59 (0.28), residues: 376 loop : -1.46 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 671 TYR 0.032 0.002 TYR D 479 PHE 0.042 0.003 PHE A 533 TRP 0.016 0.002 TRP B 607 HIS 0.010 0.002 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.24 (21561) covalent geometry : angle 0.79554 / 0.45 (29533) SS BOND : bond 0.00700 / 0.52 ( 14) SS BOND : angle 3.30181 / 2.48 ( 28) hydrogen bonds : bond 0.05161 / 3.74 ( 946) hydrogen bonds : angle 4.32317 / 3.27 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6688.44 seconds wall clock time: 114 minutes 21.64 seconds (6861.64 seconds total)