Starting phenix.real_space_refine on Mon Aug 25 12:09:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuy_43544/08_2025/8vuy_43544.map" } resolution = 3.81 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3056 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16396 2.51 5 N 4446 2.21 5 O 4687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25643 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5917 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 34, 'TRANS': 765} Chain breaks: 1 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 11, 'HIS:plan': 2, 'GLU:plan': 27, 'GLN:plan1': 4, 'TRP:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 18, 'PHE:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 305 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5760 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 29, 'HIS:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 4, 'TYR:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 300 Chain: "C" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5601 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 690 Unresolved non-hydrogen angles: 865 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 15, 'ARG:plan': 14, 'HIS:plan': 4, 'GLU:plan': 28, 'GLN:plan1': 12, 'ASP:plan': 20, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 409 Chain: "D" Number of atoms: 5445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5445 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 227} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 776 Unresolved non-hydrogen angles: 985 Unresolved non-hydrogen dihedrals: 621 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 35, 'HIS:plan': 5, 'PHE:plan': 8, 'ARG:plan': 6, 'GLN:plan1': 7, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 428 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 829 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 731 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "K" Number of atoms: 626 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 621 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 2, 'GLN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 101 Conformer: "B" Number of residues, atoms: 108, 621 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 2, 'GLN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 101 bond proxies already assigned to first conformer: 627 Chain: "L" Number of atoms: 734 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 724 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 108, 724 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 727 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS K 8 " occ=0.54 ... (8 atoms not shown) pdb=" CB BHIS K 8 " occ=0.46 residue: pdb=" N AHIS L 8 " occ=0.34 ... (18 atoms not shown) pdb=" NE2BHIS L 8 " occ=0.66 Time building chain proxies: 7.52, per 1000 atoms: 0.29 Number of scatterers: 25643 At special positions: 0 Unit cell: (130.112, 216.568, 178.904, 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 114 16.00 O 4687 8.00 N 4446 7.00 C 16396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 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 B 86 " - pdb=" SG CYS B 321 " 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 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 50 sheets defined 38.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.607A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.103A 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 143 through 146 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.518A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.514A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.994A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.612A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.863A pdb=" N ASP A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.677A pdb=" N MET A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 505 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.531A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 655 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.849A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.618A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.518A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.536A pdb=" N THR A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 812 removed outlier: 3.907A pdb=" N ASN A 812 " --> pdb=" O THR A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 813 through 841 removed outlier: 4.721A pdb=" N ILE A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.885A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.071A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.694A pdb=" N SER B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.548A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.691A pdb=" N ILE B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.595A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 removed outlier: 4.037A pdb=" N PHE B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 417 " --> pdb=" O ALA B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 417' Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.522A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 4.004A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.894A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.865A 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 548 through 552 Processing helix chain 'B' and resid 556 through 579 removed outlier: 4.534A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 625 through 657 removed outlier: 3.512A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 700 through 708 Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 772 through 786 Processing helix chain 'B' and resid 787 through 798 removed outlier: 3.774A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 798 " --> pdb=" O ALA B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.684A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.833A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 removed outlier: 3.601A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.422A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 removed outlier: 4.019A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.751A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.581A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.003A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 4.119A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 4.209A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.554A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 584 Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 626 through 655 Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.976A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 669 through 674' Processing helix chain 'C' and resid 687 through 695 removed outlier: 4.041A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.817A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.502A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 782 Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'C' and resid 809 through 841 removed outlier: 4.121A pdb=" N MET C 813 " --> pdb=" O THR C 809 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 80 through 92 removed outlier: 4.209A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.837A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.570A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.524A pdb=" N LEU D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.835A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 332 through 338 removed outlier: 4.105A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 removed outlier: 3.533A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.572A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 579 removed outlier: 3.987A pdb=" N MET D 561 " --> pdb=" O ASP D 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 657 removed outlier: 3.938A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.599A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 772 through 787 removed outlier: 3.812A pdb=" N GLY D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 797 Processing helix chain 'D' and resid 814 through 817 Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.267A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.858A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 86 removed outlier: 3.552A pdb=" N GLU K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.839A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.265A 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 194 removed outlier: 6.432A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 402 removed outlier: 3.658A pdb=" N LEU A 398 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 removed outlier: 3.513A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 removed outlier: 3.511A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.040A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 72 removed outlier: 3.583A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.756A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 342 through 344 removed outlier: 3.615A pdb=" N LEU B 349 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 365 through 367 Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 410 removed outlier: 7.503A pdb=" N LEU B 406 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TYR B 479 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 420 removed outlier: 4.080A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 437 through 438 Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.745A pdb=" N THR B 532 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.931A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 64 removed outlier: 8.683A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 166 through 168 removed outlier: 3.641A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 218 through 219 Processing sheet with id=AC4, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.847A pdb=" N GLN C 270 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 352 " --> pdb=" O GLN C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.587A pdb=" N VAL C 362 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 365 through 366 removed outlier: 3.920A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 399 through 402 removed outlier: 5.914A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AC9, first strand: chain 'C' and resid 488 through 489 removed outlier: 3.779A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 512 through 513 removed outlier: 4.291A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.288A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 70 through 72 removed outlier: 8.708A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 199 through 204 removed outlier: 8.278A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 363 through 367 removed outlier: 6.895A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.853A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.637A pdb=" N GLU D 420 " --> pdb=" O CYS D 456 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 437 through 439 removed outlier: 3.864A pdb=" N LYS D 438 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 513 through 514 removed outlier: 4.632A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 730 through 732 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.875A pdb=" N PHE H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AE4, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'J' and resid 70 through 73 removed outlier: 3.756A pdb=" N ASP J 73 " --> pdb=" O GLN J 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.977A pdb=" N THR K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.977A pdb=" N THR K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER K 93 " --> pdb=" O VAL K 100 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AF4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.925A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 35 " --> pdb=" O GLN L 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.925A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 35 " --> pdb=" O GLN L 92 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 2973 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: 4.83 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8402 1.35 - 1.47: 6494 1.47 - 1.59: 11133 1.59 - 1.71: 1 1.71 - 1.83: 182 Bond restraints: 26212 Sorted by residual: bond pdb=" CG PRO D 270 " pdb=" CD PRO D 270 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.20e+01 bond pdb=" CB PRO A 305 " pdb=" CG PRO A 305 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.72e+00 bond pdb=" C ALA D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 1.334 1.347 -0.014 8.40e-03 1.42e+04 2.62e+00 bond pdb=" CB ASP C 765 " pdb=" CG ASP C 765 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" N PRO A 305 " pdb=" CD PRO A 305 " ideal model delta sigma weight residual 1.473 1.491 -0.018 1.40e-02 5.10e+03 1.64e+00 ... (remaining 26207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 35513 2.75 - 5.50: 237 5.50 - 8.26: 41 8.26 - 11.01: 11 11.01 - 13.76: 2 Bond angle restraints: 35804 Sorted by residual: angle pdb=" CA PRO A 305 " pdb=" N PRO A 305 " pdb=" CD PRO A 305 " ideal model delta sigma weight residual 112.00 99.05 12.95 1.40e+00 5.10e-01 8.56e+01 angle pdb=" N PRO D 270 " pdb=" CD PRO D 270 " pdb=" CG PRO D 270 " ideal model delta sigma weight residual 103.20 89.44 13.76 1.50e+00 4.44e-01 8.42e+01 angle pdb=" CA PRO D 270 " pdb=" N PRO D 270 " pdb=" CD PRO D 270 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.75e+01 angle pdb=" CA PRO D 270 " pdb=" CB PRO D 270 " pdb=" CG PRO D 270 " ideal model delta sigma weight residual 104.50 94.31 10.19 1.90e+00 2.77e-01 2.88e+01 angle pdb=" N VAL B 42 " pdb=" CA VAL B 42 " pdb=" C VAL B 42 " ideal model delta sigma weight residual 113.20 108.14 5.06 9.60e-01 1.09e+00 2.78e+01 ... (remaining 35799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 13317 17.77 - 35.54: 1575 35.54 - 53.31: 409 53.31 - 71.08: 58 71.08 - 88.85: 32 Dihedral angle restraints: 15391 sinusoidal: 4955 harmonic: 10436 Sorted by residual: dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 -178.15 -88.85 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -173.54 87.54 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -163.45 77.45 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 15388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3707 0.068 - 0.136: 453 0.136 - 0.205: 4 0.205 - 0.273: 3 0.273 - 0.341: 2 Chirality restraints: 4169 Sorted by residual: chirality pdb=" CG LEU C 632 " pdb=" CB LEU C 632 " pdb=" CD1 LEU C 632 " pdb=" CD2 LEU C 632 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CG LEU D 567 " pdb=" CB LEU D 567 " pdb=" CD1 LEU D 567 " pdb=" CD2 LEU D 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE A 513 " pdb=" CA ILE A 513 " pdb=" CG1 ILE A 513 " pdb=" CG2 ILE A 513 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4166 not shown) Planarity restraints: 4607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 304 " -0.095 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO A 305 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 556 " -0.062 5.00e-02 4.00e+02 9.50e-02 1.45e+01 pdb=" N PRO A 557 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 515 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 516 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " 0.028 5.00e-02 4.00e+02 ... (remaining 4604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 375 2.66 - 3.22: 23813 3.22 - 3.78: 37042 3.78 - 4.34: 44012 4.34 - 4.90: 75360 Nonbonded interactions: 180602 Sorted by model distance: nonbonded pdb=" OH TYR B 389 " pdb=" O TYR B 452 " model vdw 2.099 3.040 nonbonded pdb=" OH TYR B 164 " pdb=" O TYR B 388 " model vdw 2.186 3.040 nonbonded pdb=" O THR C 396 " pdb=" OG1 THR C 473 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLN A 742 " pdb=" OH TYR A 795 " model vdw 2.217 3.040 nonbonded pdb=" O SER B 753 " pdb=" OG SER B 753 " model vdw 2.240 3.040 ... (remaining 180597 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 29 and (name N or name CA or name C or name O \ or name CB )) or (resid 30 through 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 through 45 or (resid 46 through 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or (resid 58 through 63 and \ (name N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 th \ rough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 or \ (resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 \ or (resid 70 through 72 and (name N or name CA or name C or name O or name CB )) \ or resid 73 or (resid 74 through 75 and (name N or name CA or name C or name O \ or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 83 or (resid 84 through 86 and (n \ ame N or name CA or name C or name O or name CB )) or resid 87 through 100 or (r \ esid 101 through 103 and (name N or name CA or name C or name O or name CB )) or \ resid 104 or (resid 105 and (name N or name CA or name C or name O or name CB ) \ ) or resid 106 or (resid 107 through 108 and (name N or name CA or name C or nam \ e O or name CB )) or resid 109 or (resid 110 through 111 and (name N or name CA \ or name C or name O or name CB )) or resid 112 through 122 or (resid 123 through \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 128 or (resid 129 through 132 and (name N or name CA or name C or name O or n \ ame CB )) or resid 133 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 or (resid 155 and (name N or name CA or n \ ame C or name O or name CB )) or resid 156 through 160 or (resid 161 and (name N \ or name CA or name C or name O or name CB )) or resid 162 through 170 or (resid \ 171 through 172 and (name N or name CA or name C or name O or name CB )) or res \ id 173 through 177 or (resid 178 and (name N or name CA or name C or name O or n \ ame CB )) or resid 179 through 204 or (resid 205 through 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 239 or (resid 240 and \ (name N or name CA or name C or name O or name CB )) or resid 241 through 248 o \ r (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 50 or (resid 251 through 253 and (name N or name CA or name C or name O or name \ CB )) or resid 254 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or name \ C or name O or name CB )) or resid 278 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 or (resid 283 through 285 \ and (name N or name CA or name C or name O or name CB )) or resid 286 or (resid \ 287 through 292 and (name N or name CA or name C or name O or name CB )) or res \ id 293 through 294 or (resid 295 and (name N or name CA or name C or name O or n \ ame CB )) or resid 296 through 299 or (resid 300 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 through 305 or (resid 306 and \ (name N or name CA or name C or name O or name CB )) or resid 307 through 310 o \ r (resid 311 through 313 and (name N or name CA or name C or name O or name CB ) \ ) or resid 314 through 319 or (resid 320 and (name N or name CA or name C or nam \ e O or name CB )) or resid 321 through 323 or (resid 324 through 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 331 or (resid \ 332 and (name N or name CA or name C or name O or name CB )) or resid 333 throu \ gh 334 or (resid 335 and (name N or name CA or name C or name O or name CB )) or \ resid 336 through 340 or (resid 341 through 343 and (name N or name CA or name \ C or name O or name CB )) or resid 344 through 346 or (resid 347 and (name N or \ name CA or name C or name O or name CB )) or resid 348 through 353 or (resid 354 \ and (name N or name CA or name C or name O or name CB )) or resid 355 through 3 \ 91 or (resid 392 through 395 and (name N or name CA or name C or name O or name \ CB )) or resid 396 through 414 or (resid 415 through 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 425 or (resid 426 through \ 427 and (name N or name CA or name C or name O or name CB )) or resid 428 throu \ gh 486 or (resid 487 through 492 and (name N or name CA or name C or name O or n \ ame CB )) or resid 493 through 495 or (resid 496 through 497 and (name N or name \ CA or name C or name O or name CB )) or resid 498 through 527 or (resid 528 and \ (name N or name CA or name C or name O or name CB )) or resid 529 through 535 o \ r (resid 536 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 37 through 548 or (resid 549 and (name N or name CA or name C or name O or name \ CB )) or resid 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 555 or (resid 556 and (name N or name \ CA or name C or name O or name CB )) or resid 557 through 558 or (resid 559 and \ (name N or name CA or name C or name O or name CB )) or resid 560 through 567 o \ r (resid 568 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 69 through 571 or (resid 572 through 574 and (name N or name CA or name C or nam \ e O or name CB )) or resid 575 or (resid 576 and (name N or name CA or name C or \ name O or name CB )) or resid 577 through 603 or (resid 604 and (name N or name \ CA or name C or name O or name CB )) or resid 605 through 618 or (resid 619 and \ (name N or name CA or name C or name O or name CB )) or resid 620 through 677 o \ r (resid 678 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 79 through 712 or (resid 713 through 717 and (name N or name CA or name C or nam \ e O or name CB )) or resid 718 through 768 or (resid 769 and (name N or name CA \ or name C or name O or name CB )) or resid 770 through 795 or (resid 796 and (na \ me N or name CA or name C or name O or name CB )) or resid 797 through 798 or (r \ esid 799 and (name N or name CA or name C or name O or name CB )) or resid 800 t \ hrough 808 or (resid 809 and (name N or name CA or name C or name O or name CB ) \ ) or resid 810 or (resid 811 through 814 and (name N or name CA or name C or nam \ e O or name CB )) or resid 815 through 818 or (resid 819 through 821 and (name N \ or name CA or name C or name O or name CB )) or resid 822 through 823 or (resid \ 824 through 826 and (name N or name CA or name C or name O or name CB )) or res \ id 827 or (resid 828 through 841 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 25 through 225 or (resid 226 through 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 through 405 or (resid 406 a \ nd (name N or name CA or name C or name O or name CB )) or resid 407 through 415 \ or (resid 416 through 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 through 494 or (resid 495 through 497 and (name N or name CA or \ name C or name O or name CB )) or resid 498 through 547 or (resid 548 through 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 578 or (resid 579 and (name N or name CA or name C or name O or name CB )) or r \ esid 580 through 606 or (resid 607 and (name N or name CA or name C or name O or \ name CB )) or resid 608 through 661 or (resid 662 and (name N or name CA or nam \ e C or name O or name CB )) or resid 663 through 694 or (resid 695 and (name N o \ r name CA or name C or name O or name CB )) or resid 696 through 697 or (resid 6 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 699 through \ 706 or (resid 707 and (name N or name CA or name C or name O or name CB )) or r \ esid 708 through 715 or (resid 716 through 717 and (name N or name CA or name C \ or name O or name CB )) or resid 718 through 736 or (resid 737 and (name N or na \ me CA or name C or name O or name CB )) or resid 738 through 742 or (resid 743 a \ nd (name N or name CA or name C or name O or name CB )) or resid 744 through 785 \ or (resid 786 and (name N or name CA or name C or name O or name CB )) or resid \ 787 through 841)) } ncs_group { reference = (chain 'B' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 or (resid 37 through 42 and (name N or name CA or name C or name \ O or name CB )) or resid 43 or (resid 44 through 57 and (name N or name CA or na \ me C or name O or name CB )) or resid 58 or (resid 59 through 65 and (name N or \ name CA or name C or name O or name CB )) or resid 66 or (resid 67 through 73 an \ d (name N or name CA or name C or name O or name CB )) or resid 74 through 80 or \ (resid 81 through 82 and (name N or name CA or name C or name O or name CB )) o \ r resid 83 through 84 or (resid 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 through 90 or (resid 91 through 95 and (name N or name C \ A or name C or name O or name CB )) or resid 96 or (resid 97 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 102 or (res \ id 103 through 104 and (name N or name CA or name C or name O or name CB )) or r \ esid 105 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 through 122 or (resid 123 and (name N o \ r name CA or name C or name O or name CB )) or resid 124 through 129 or (resid 1 \ 30 through 133 and (name N or name CA or name C or name O or name CB )) or resid \ 134 through 137 or (resid 138 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 or (resid 141 through 142 and (name N or name C \ A or name C or name O or name CB )) or resid 143 through 149 or (resid 150 throu \ gh 151 and (name N or name CA or name C or name O or name CB )) or resid 152 thr \ ough 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) \ or resid 158 through 160 or (resid 161 and (name N or name CA or name C or name \ O or name CB )) or resid 162 through 167 or (resid 168 and (name N or name CA or \ name C or name O or name CB )) or resid 169 or (resid 170 and (name N or name C \ A or name C or name O or name CB )) or resid 171 or (resid 172 through 174 and ( \ name N or name CA or name C or name O or name CB )) or resid 175 through 180 or \ (resid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ or (resid 183 and (name N or name CA or name C or name O or name CB )) or resid \ 184 through 188 or (resid 189 through 190 and (name N or name CA or name C or n \ ame O or name CB )) or resid 191 through 202 or (resid 203 and (name N or name C \ A or name C or name O or name CB )) or resid 204 through 213 or (resid 214 throu \ gh 216 and (name N or name CA or name C or name O or name CB )) or resid 217 thr \ ough 222 or (resid 223 through 224 and (name N or name CA or name C or name O or \ name CB )) or resid 225 through 227 or (resid 228 and (name N or name CA or nam \ e C or name O or name CB )) or resid 229 through 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 241 or (resid 2 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 243 through \ 246 or (resid 247 and (name N or name CA or name C or name O or name CB )) or r \ esid 248 or (resid 249 through 250 and (name N or name CA or name C or name O or \ name CB )) or resid 251 through 253 or (resid 254 through 255 and (name N or na \ me CA or name C or name O or name CB )) or resid 256 through 260 or (resid 261 t \ hrough 263 and (name N or name CA or name C or name O or name CB )) or resid 264 \ or (resid 265 through 267 and (name N or name CA or name C or name O or name CB \ )) or resid 268 through 270 or (resid 271 through 273 and (name N or name CA or \ name C or name O or name CB )) or resid 274 through 276 or (resid 277 through 2 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 281 through \ 282 or (resid 283 through 284 and (name N or name CA or name C or name O or nam \ e CB )) or resid 285 through 288 or (resid 289 and (name N or name CA or name C \ or name O or name CB )) or resid 290 through 292 or (resid 293 and (name N or na \ me CA or name C or name O or name CB )) or resid 294 or (resid 295 and (name N o \ r name CA or name C or name O or name CB )) or resid 296 or (resid 297 through 2 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 300 through \ 306 or (resid 307 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 332 or (resid 333 through 335 and (name N or name C \ A or name C or name O or name CB )) or resid 336 through 338 or (resid 339 throu \ gh 340 and (name N or name CA or name C or name O or name CB )) or resid 341 or \ (resid 342 through 343 and (name N or name CA or name C or name O or name CB )) \ or resid 344 through 347 or (resid 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 or (resid 350 through 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 364 or (resid 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 and ( \ name N or name CA or name C or name O or name CB )) or resid 368 through 370 or \ (resid 371 through 372 and (name N or name CA or name C or name O or name CB )) \ or resid 373 through 375 or (resid 376 and (name N or name CA or name C or name \ O or name CB )) or resid 377 through 379 or (resid 380 through 381 and (name N o \ r name CA or name C or name O or name CB )) or resid 382 through 385 or (resid 3 \ 86 through 387 and (name N or name CA or name C or name O or name CB )) or resid \ 388 through 389 or (resid 390 and (name N or name CA or name C or name O or nam \ e CB )) or resid 391 through 392 or (resid 393 through 403 and (name N or name C \ A or name C or name O or name CB )) or resid 404 through 445 or (resid 446 throu \ gh 449 and (name N or name CA or name C or name O or name CB )) or resid 450 thr \ ough 451 or (resid 452 and (name N or name CA or name C or name O or name CB )) \ or resid 453 through 469 or (resid 470 and (name N or name CA or name C or name \ O or name CB )) or resid 471 through 481 or (resid 482 and (name N or name CA or \ name C or name O or name CB )) or resid 483 through 523 or (resid 524 and (name \ N or name CA or name C or name O or name CB )) or resid 525 through 556 or (res \ id 557 and (name N or name CA or name C or name O or name CB )) or resid 558 thr \ ough 562 or (resid 563 through 565 and (name N or name CA or name C or name O or \ name CB )) or resid 566 through 573 or (resid 574 through 579 and (name N or na \ me CA or name C or name O or name CB )) or resid 599 through 600 or (resid 601 t \ hrough 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 through 617 or (resid 618 and (name N or name CA or name C or n \ ame O or name CB )) or resid 619 through 658 or (resid 659 and (name N or name C \ A or name C or name O or name CB )) or resid 660 through 669 or (resid 670 and ( \ name N or name CA or name C or name O or name CB )) or resid 671 through 721 or \ (resid 722 and (name N or name CA or name C or name O or name CB )) or resid 723 \ through 776 or (resid 777 and (name N or name CA or name C or name O or name CB \ )) or resid 778 through 787 or (resid 788 and (name N or name CA or name C or n \ ame O or name CB )) or resid 789 or (resid 790 through 791 and (name N or name C \ A or name C or name O or name CB )) or resid 792 through 802 or (resid 803 throu \ gh 812 and (name N or name CA or name C or name O or name CB )) or resid 813 thr \ ough 828 or (resid 829 through 831 and (name N or name CA or name C or name O or \ name CB )) or resid 832 through 835 or (resid 836 and (name N or name CA or nam \ e C or name O or name CB )) or resid 837 through 839 or (resid 840 through 845 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 35 through 221 or (resid 222 through 224 and (name N or na \ me CA or name C or name O or name CB )) or resid 225 through 244 or (resid 245 a \ nd (name N or name CA or name C or name O or name CB )) or resid 246 through 285 \ or (resid 286 and (name N or name CA or name C or name O or name CB )) or resid \ 287 through 313 or (resid 314 and (name N or name CA or name C or name O or nam \ e CB )) or resid 315 through 318 or (resid 319 through 320 and (name N or name C \ A or name C or name O or name CB )) or resid 321 through 329 or (resid 330 throu \ gh 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thr \ ough 424 or (resid 425 and (name N or name CA or name C or name O or name CB )) \ or resid 426 through 489 or (resid 490 and (name N or name CA or name C or name \ O or name CB )) or resid 491 through 516 or (resid 517 and (name N or name CA or \ name C or name O or name CB )) or resid 518 through 543 or (resid 544 through 5 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 561 or (resid 562 through 565 and (name N or name CA or name C or name O or nam \ e CB )) or resid 566 through 567 or (resid 568 and (name N or name CA or name C \ or name O or name CB )) or resid 569 or (resid 570 through 571 and (name N or na \ me CA or name C or name O or name CB )) or resid 572 through 601 or (resid 602 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 603 through 60 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 607 through \ 608 or (resid 609 and (name N or name CA or name C or name O or name CB )) or re \ sid 610 through 661 or (resid 662 and (name N or name CA or name C or name O or \ name CB )) or resid 663 through 668 or (resid 669 through 670 and (name N or nam \ e CA or name C or name O or name CB )) or resid 671 through 672 or (resid 673 an \ d (name N or name CA or name C or name O or name CB )) or resid 674 through 677 \ or (resid 678 and (name N or name CA or name C or name O or name CB )) or resid \ 679 through 731 or (resid 732 through 734 and (name N or name CA or name C or na \ me O or name CB )) or resid 735 through 785 or (resid 786 and (name N or name CA \ or name C or name O or name CB )) or resid 787 through 790 or (resid 791 and (n \ ame N or name CA or name C or name O or name CB )) or resid 792 through 809 or ( \ resid 810 through 812 and (name N or name CA or name C or name O or name CB )) o \ r resid 813 or (resid 814 and (name N or name CA or name C or name O or name CB \ )) or resid 815 through 830 or (resid 831 and (name N or name CA or name C or na \ me O or name CB )) or resid 832 through 840 or (resid 841 through 845 and (name \ N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or (resid 8 through 21 and (name N or name CA or name C or name O or \ name CB )) or resid 22 or (resid 23 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 27 or (resid 28 through 30 and (nam \ e N or name CA or name C or name O or name CB )) or resid 31 through 37 or (resi \ d 38 through 40 and (name N or name CA or name C or name O or name CB )) or resi \ d 41 through 45 or (resid 46 through 47 and (name N or name CA or name C or name \ O or name CB )) or resid 48 through 50 or (resid 51 through 52 and (name N or n \ ame CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 and \ (name N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 a \ nd (name N or name CA or name C or name O or name CB )) or resid 66 or (resid 67 \ through 68 and (name N or name CA or name C or name O or name CB )) or resid 69 \ through 77 or (resid 78 and (name N or name CA or name C or name O or name CB ) \ ) or resid 79 through 82 or (resid 83 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 116)) selection = (chain 'J' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 116)) } ncs_group { reference = (chain 'K' and (resid 1 through 7 or resid 9 through 108)) selection = (chain 'L' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 or resid 9 or (resid 10 through 14 and (name N or name CA \ or name C or name O or name CB )) or (resid 15 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 or (resid 23 through 26 and (nam \ e N or name CA or name C or name O or name CB )) or resid 27 through 28 or (resi \ d 29 through 32 and (name N or name CA or name C or name O or name CB )) or resi \ d 33 or (resid 34 through 35 and (name N or name CA or name C or name O or name \ CB )) or resid 36 through 38 or (resid 39 through 40 and (name N or name CA or n \ ame C or name O or name CB )) or resid 41 through 42 or (resid 43 through 44 and \ (name N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 t \ hrough 49 and (name N or name CA or name C or name O or name CB )) or resid 50 o \ r (resid 51 through 52 and (name N or name CA or name C or name O or name CB )) \ or resid 53 or (resid 54 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 66 or (resid 67 through 79 and (na \ me N or name CA or name C or name O or name CB )) or (resid 80 through 88 and (n \ ame N or name CA or name C or name O or name CB )) or resid 89 through 91 or (re \ sid 92 and (name N or name CA or name C or name O or name CB )) or resid 93 thro \ ugh 97 or (resid 98 through 100 and (name N or name CA or name C or name O or na \ me CB )) or resid 101 through 108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.270 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 26230 Z= 0.119 Angle : 0.624 13.761 35840 Z= 0.322 Chirality : 0.043 0.341 4169 Planarity : 0.004 0.133 4607 Dihedral : 16.768 88.490 8615 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.35 % Favored : 92.51 % Rotamer: Outliers : 0.22 % Allowed : 38.39 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.85 (0.15), residues: 3586 helix: 2.06 (0.15), residues: 1193 sheet: -0.87 (0.23), residues: 555 loop : -2.40 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 84 TYR 0.020 0.001 TYR A 330 PHE 0.025 0.001 PHE C 639 TRP 0.025 0.001 TRP C 636 HIS 0.003 0.000 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00277 (26212) covalent geometry : angle 0.62291 (35804) SS BOND : bond 0.00286 ( 18) SS BOND : angle 1.31480 ( 36) hydrogen bonds : bond 0.19050 ( 1037) hydrogen bonds : angle 5.92265 ( 2973) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 369 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 HIS cc_start: 0.7354 (t70) cc_final: 0.7108 (t70) REVERT: C 607 MET cc_start: 0.8279 (ppp) cc_final: 0.7936 (ppp) outliers start: 5 outliers final: 5 residues processed: 372 average time/residue: 0.1503 time to fit residues: 94.5250 Evaluate side-chains 361 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 356 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.173094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.140168 restraints weight = 47971.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136132 restraints weight = 73463.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132865 restraints weight = 67048.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133824 restraints weight = 61781.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133209 restraints weight = 47188.663| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26230 Z= 0.136 Angle : 0.575 8.257 35840 Z= 0.297 Chirality : 0.043 0.275 4169 Planarity : 0.004 0.062 4607 Dihedral : 4.149 45.160 3827 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 4.51 % Allowed : 34.36 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.85 (0.15), residues: 3586 helix: 1.96 (0.15), residues: 1233 sheet: -0.91 (0.23), residues: 554 loop : -2.40 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 439 TYR 0.019 0.001 TYR A 330 PHE 0.019 0.001 PHE C 472 TRP 0.031 0.001 TRP D 379 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00309 (26212) covalent geometry : angle 0.57420 (35804) SS BOND : bond 0.00275 ( 18) SS BOND : angle 1.17108 ( 36) hydrogen bonds : bond 0.04332 ( 1037) hydrogen bonds : angle 4.72990 ( 2973) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 372 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7080 (OUTLIER) cc_final: 0.6794 (p) REVERT: A 221 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 60 HIS cc_start: 0.7347 (t70) cc_final: 0.7069 (t70) REVERT: B 240 ILE cc_start: 0.9208 (mt) cc_final: 0.8889 (mm) REVERT: B 406 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8581 (pp) REVERT: B 488 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8707 (pttt) REVERT: C 607 MET cc_start: 0.8303 (ppp) cc_final: 0.7940 (ppp) REVERT: C 780 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7653 (t70) outliers start: 104 outliers final: 62 residues processed: 446 average time/residue: 0.1502 time to fit residues: 112.9413 Evaluate side-chains 414 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 347 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 802 HIS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 355 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 350 optimal weight: 0.0170 chunk 206 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.173660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141152 restraints weight = 48234.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136820 restraints weight = 70761.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133098 restraints weight = 65579.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134073 restraints weight = 63841.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.133738 restraints weight = 44211.997| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26230 Z= 0.118 Angle : 0.562 9.347 35840 Z= 0.288 Chirality : 0.042 0.231 4169 Planarity : 0.004 0.049 4607 Dihedral : 4.050 47.667 3823 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 5.03 % Allowed : 34.45 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.83 (0.15), residues: 3586 helix: 2.01 (0.15), residues: 1228 sheet: -1.03 (0.23), residues: 550 loop : -2.36 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.020 0.001 TYR J 53 PHE 0.022 0.001 PHE B 550 TRP 0.033 0.001 TRP L 36 HIS 0.009 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00270 (26212) covalent geometry : angle 0.55791 (35804) SS BOND : bond 0.00504 ( 18) SS BOND : angle 2.18484 ( 36) hydrogen bonds : bond 0.03712 ( 1037) hydrogen bonds : angle 4.50377 ( 2973) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 365 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6799 (mmm) cc_final: 0.6534 (mmm) REVERT: A 221 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 817 PHE cc_start: 0.7589 (m-80) cc_final: 0.7379 (m-80) REVERT: B 132 MET cc_start: 0.7359 (tmm) cc_final: 0.7143 (tmm) REVERT: B 406 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8527 (pp) REVERT: B 600 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: C 607 MET cc_start: 0.8366 (ppp) cc_final: 0.8009 (ppp) REVERT: C 780 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.7860 (t70) outliers start: 116 outliers final: 77 residues processed: 449 average time/residue: 0.1482 time to fit residues: 113.1256 Evaluate side-chains 434 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 353 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 802 HIS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 56 optimal weight: 0.0270 chunk 311 optimal weight: 50.0000 chunk 337 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.173956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.141707 restraints weight = 47938.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137557 restraints weight = 70760.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133885 restraints weight = 69980.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134847 restraints weight = 62755.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134611 restraints weight = 46495.215| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26230 Z= 0.112 Angle : 0.557 9.193 35840 Z= 0.283 Chirality : 0.042 0.241 4169 Planarity : 0.004 0.048 4607 Dihedral : 4.000 50.124 3823 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 5.60 % Allowed : 33.75 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.79 (0.15), residues: 3586 helix: 2.06 (0.15), residues: 1230 sheet: -1.02 (0.23), residues: 555 loop : -2.35 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.023 0.001 TYR J 53 PHE 0.019 0.001 PHE B 550 TRP 0.021 0.001 TRP L 36 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00256 (26212) covalent geometry : angle 0.55476 (35804) SS BOND : bond 0.00603 ( 18) SS BOND : angle 1.64210 ( 36) hydrogen bonds : bond 0.03421 ( 1037) hydrogen bonds : angle 4.35916 ( 2973) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 373 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8382 (pt) REVERT: A 74 MET cc_start: 0.6997 (mmm) cc_final: 0.6764 (mmm) REVERT: A 221 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 470 MET cc_start: 0.7306 (mmm) cc_final: 0.6691 (mmt) REVERT: A 817 PHE cc_start: 0.7598 (m-80) cc_final: 0.7297 (m-80) REVERT: B 406 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 398 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8149 (pp) REVERT: C 607 MET cc_start: 0.8381 (ppp) cc_final: 0.7953 (ppp) REVERT: C 754 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8546 (p90) REVERT: C 780 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7837 (t70) REVERT: D 706 MET cc_start: 0.8158 (ttp) cc_final: 0.7939 (ttt) outliers start: 129 outliers final: 88 residues processed: 466 average time/residue: 0.1470 time to fit residues: 116.7711 Evaluate side-chains 454 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 360 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 802 HIS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 249 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 158 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 205 optimal weight: 0.1980 chunk 209 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 310 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 350 GLN D 127 HIS H 33 ASN J 57 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.174539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.142478 restraints weight = 47806.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138305 restraints weight = 69712.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134831 restraints weight = 62204.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135527 restraints weight = 60810.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134898 restraints weight = 41964.800| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26230 Z= 0.105 Angle : 0.555 8.710 35840 Z= 0.281 Chirality : 0.042 0.274 4169 Planarity : 0.004 0.048 4607 Dihedral : 3.953 52.617 3823 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.43 % Favored : 92.43 % Rotamer: Outliers : 5.16 % Allowed : 34.58 % Favored : 60.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 3586 helix: 2.11 (0.15), residues: 1231 sheet: -0.99 (0.23), residues: 559 loop : -2.32 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.012 0.001 TYR L 90 PHE 0.017 0.001 PHE D 550 TRP 0.016 0.001 TRP L 36 HIS 0.007 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00239 (26212) covalent geometry : angle 0.55409 (35804) SS BOND : bond 0.00446 ( 18) SS BOND : angle 1.15835 ( 36) hydrogen bonds : bond 0.03194 ( 1037) hydrogen bonds : angle 4.25856 ( 2973) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 374 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (pt) REVERT: A 74 MET cc_start: 0.6974 (mmm) cc_final: 0.6739 (mmm) REVERT: A 221 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 817 PHE cc_start: 0.7479 (m-80) cc_final: 0.7170 (m-80) REVERT: B 406 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8487 (pp) REVERT: B 600 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: C 184 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (mm) REVERT: C 398 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8136 (pp) REVERT: C 607 MET cc_start: 0.8314 (ppp) cc_final: 0.7883 (ppp) REVERT: C 754 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8483 (p90) REVERT: C 780 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7836 (t70) REVERT: J 55 SER cc_start: 0.7471 (p) cc_final: 0.7184 (p) outliers start: 119 outliers final: 84 residues processed: 457 average time/residue: 0.1508 time to fit residues: 116.2688 Evaluate side-chains 450 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 358 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 115 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 50.0000 chunk 354 optimal weight: 0.7980 chunk 42 optimal weight: 0.0670 chunk 255 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 170 optimal weight: 3.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN H 33 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.175810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.142984 restraints weight = 48184.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137878 restraints weight = 70855.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133851 restraints weight = 68692.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135367 restraints weight = 58157.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134686 restraints weight = 42693.770| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26230 Z= 0.097 Angle : 0.564 9.736 35840 Z= 0.283 Chirality : 0.042 0.259 4169 Planarity : 0.004 0.046 4607 Dihedral : 3.866 54.666 3823 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.01 % Favored : 92.85 % Rotamer: Outliers : 4.56 % Allowed : 35.05 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.67 (0.15), residues: 3586 helix: 2.14 (0.15), residues: 1233 sheet: -0.91 (0.23), residues: 558 loop : -2.30 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 294 TYR 0.015 0.001 TYR A 330 PHE 0.017 0.001 PHE D 550 TRP 0.050 0.001 TRP L 36 HIS 0.008 0.000 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00214 (26212) covalent geometry : angle 0.56248 (35804) SS BOND : bond 0.00454 ( 18) SS BOND : angle 1.49617 ( 36) hydrogen bonds : bond 0.02952 ( 1037) hydrogen bonds : angle 4.16608 ( 2973) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 369 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8394 (pt) REVERT: A 74 MET cc_start: 0.7175 (mmm) cc_final: 0.6926 (mmm) REVERT: A 221 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 817 PHE cc_start: 0.7326 (m-80) cc_final: 0.7082 (m-80) REVERT: B 406 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 600 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5613 (m-80) REVERT: C 184 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7971 (mm) REVERT: C 398 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 754 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8505 (p90) REVERT: C 780 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7870 (t70) outliers start: 105 outliers final: 72 residues processed: 444 average time/residue: 0.1499 time to fit residues: 112.7067 Evaluate side-chains 438 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 60 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 183 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 239 optimal weight: 40.0000 chunk 356 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS H 33 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.172462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140058 restraints weight = 47551.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136586 restraints weight = 74856.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134162 restraints weight = 63373.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134484 restraints weight = 63185.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133982 restraints weight = 46814.985| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26230 Z= 0.161 Angle : 0.606 10.040 35840 Z= 0.308 Chirality : 0.043 0.276 4169 Planarity : 0.004 0.046 4607 Dihedral : 4.081 53.594 3823 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.38 % Favored : 91.48 % Rotamer: Outliers : 5.64 % Allowed : 34.36 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.69 (0.15), residues: 3586 helix: 2.11 (0.15), residues: 1236 sheet: -0.98 (0.23), residues: 523 loop : -2.27 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.017 0.001 TYR B 356 PHE 0.021 0.001 PHE C 754 TRP 0.039 0.001 TRP L 36 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00385 (26212) covalent geometry : angle 0.60480 (35804) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.41389 ( 36) hydrogen bonds : bond 0.03715 ( 1037) hydrogen bonds : angle 4.25971 ( 2973) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 369 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8358 (pt) REVERT: A 221 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 627 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5331 (t80) REVERT: B 60 HIS cc_start: 0.7110 (t70) cc_final: 0.6798 (t70) REVERT: B 406 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8585 (pp) REVERT: C 398 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8186 (pp) REVERT: C 754 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8457 (p90) REVERT: C 780 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7885 (t70) outliers start: 130 outliers final: 95 residues processed: 466 average time/residue: 0.1446 time to fit residues: 115.7287 Evaluate side-chains 461 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 359 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 802 HIS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 264 optimal weight: 40.0000 chunk 23 optimal weight: 4.9990 chunk 343 optimal weight: 50.0000 chunk 326 optimal weight: 4.9990 chunk 175 optimal weight: 20.0000 chunk 225 optimal weight: 0.5980 chunk 233 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS B 359 HIS ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.169929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138667 restraints weight = 47758.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.136670 restraints weight = 73113.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133467 restraints weight = 53078.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131774 restraints weight = 56492.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130127 restraints weight = 51129.605| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26230 Z= 0.231 Angle : 0.671 10.558 35840 Z= 0.344 Chirality : 0.046 0.246 4169 Planarity : 0.004 0.050 4607 Dihedral : 4.482 54.042 3823 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.44 % Favored : 90.42 % Rotamer: Outliers : 6.20 % Allowed : 34.06 % Favored : 59.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.91 (0.15), residues: 3586 helix: 1.94 (0.15), residues: 1229 sheet: -1.06 (0.23), residues: 535 loop : -2.41 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 439 TYR 0.021 0.002 TYR B 356 PHE 0.026 0.002 PHE C 754 TRP 0.034 0.002 TRP L 36 HIS 0.008 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00550 (26212) covalent geometry : angle 0.66892 (35804) SS BOND : bond 0.00393 ( 18) SS BOND : angle 1.60785 ( 36) hydrogen bonds : bond 0.04433 ( 1037) hydrogen bonds : angle 4.50794 ( 2973) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 367 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8377 (pt) REVERT: A 221 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8739 (tt) REVERT: A 627 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5440 (t80) REVERT: B 406 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 398 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8261 (pp) REVERT: C 754 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8385 (p90) REVERT: C 780 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8115 (t70) outliers start: 143 outliers final: 115 residues processed: 475 average time/residue: 0.1463 time to fit residues: 119.5238 Evaluate side-chains 482 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 360 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 802 HIS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 356 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 354 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 35 optimal weight: 0.0040 chunk 116 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 238 optimal weight: 10.0000 chunk 312 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS C 780 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.173721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140471 restraints weight = 46421.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138348 restraints weight = 69694.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134840 restraints weight = 53040.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134067 restraints weight = 54122.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132517 restraints weight = 45586.733| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26230 Z= 0.113 Angle : 0.621 11.064 35840 Z= 0.310 Chirality : 0.043 0.276 4169 Planarity : 0.004 0.049 4607 Dihedral : 4.156 59.436 3823 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.46 % Favored : 92.37 % Rotamer: Outliers : 4.08 % Allowed : 36.01 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.77 (0.15), residues: 3586 helix: 2.04 (0.15), residues: 1235 sheet: -1.03 (0.23), residues: 571 loop : -2.32 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.010 0.001 TYR B 388 PHE 0.022 0.001 PHE B 550 TRP 0.034 0.001 TRP L 36 HIS 0.025 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00257 (26212) covalent geometry : angle 0.61802 (35804) SS BOND : bond 0.00343 ( 18) SS BOND : angle 2.08486 ( 36) hydrogen bonds : bond 0.03329 ( 1037) hydrogen bonds : angle 4.23734 ( 2973) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 382 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8389 (pt) REVERT: A 221 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 627 PHE cc_start: 0.6013 (OUTLIER) cc_final: 0.5342 (t80) REVERT: B 406 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8441 (pp) REVERT: C 754 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8246 (p90) REVERT: H 47 GLU cc_start: 0.6642 (pm20) cc_final: 0.6430 (pm20) REVERT: K 33 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.4701 (p90) outliers start: 94 outliers final: 76 residues processed: 458 average time/residue: 0.1460 time to fit residues: 114.0777 Evaluate side-chains 446 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 364 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 207 optimal weight: 2.9990 chunk 195 optimal weight: 0.0370 chunk 349 optimal weight: 7.9990 chunk 308 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 324 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 312 optimal weight: 0.0170 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS D 105 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.174783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141810 restraints weight = 46393.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.138142 restraints weight = 72860.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135468 restraints weight = 55464.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135341 restraints weight = 55173.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135131 restraints weight = 44729.879| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26230 Z= 0.108 Angle : 0.628 11.329 35840 Z= 0.310 Chirality : 0.044 0.290 4169 Planarity : 0.004 0.047 4607 Dihedral : 4.046 57.095 3823 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.51 % Favored : 92.35 % Rotamer: Outliers : 3.08 % Allowed : 37.05 % Favored : 59.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3586 helix: 2.03 (0.15), residues: 1241 sheet: -0.87 (0.23), residues: 564 loop : -2.25 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 156 TYR 0.011 0.001 TYR B 356 PHE 0.025 0.001 PHE C 639 TRP 0.064 0.001 TRP D 379 HIS 0.012 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00244 (26212) covalent geometry : angle 0.62514 (35804) SS BOND : bond 0.00396 ( 18) SS BOND : angle 1.86906 ( 36) hydrogen bonds : bond 0.03069 ( 1037) hydrogen bonds : angle 4.14840 ( 2973) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7172 Ramachandran restraints generated. 3586 Oldfield, 0 Emsley, 3586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 371 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (pt) REVERT: A 221 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8553 (tt) REVERT: B 406 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (pp) REVERT: C 754 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8295 (p90) REVERT: H 47 GLU cc_start: 0.6595 (pm20) cc_final: 0.6383 (pm20) REVERT: H 86 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7213 (p) REVERT: K 33 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4620 (p90) outliers start: 71 outliers final: 62 residues processed: 428 average time/residue: 0.1477 time to fit residues: 107.8916 Evaluate side-chains 435 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 367 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 754 PHE Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 811 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain K residue 33 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 329 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 336 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138644 restraints weight = 46093.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134734 restraints weight = 68706.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132260 restraints weight = 64864.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132554 restraints weight = 59923.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131856 restraints weight = 45005.924| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26230 Z= 0.186 Angle : 0.666 11.530 35840 Z= 0.332 Chirality : 0.045 0.291 4169 Planarity : 0.004 0.049 4607 Dihedral : 4.227 58.439 3823 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.52 % Favored : 91.31 % Rotamer: Outliers : 3.99 % Allowed : 36.18 % Favored : 59.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 3586 helix: 2.03 (0.15), residues: 1235 sheet: -0.87 (0.22), residues: 579 loop : -2.33 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 84 TYR 0.021 0.001 TYR B 356 PHE 0.030 0.002 PHE B 176 TRP 0.055 0.001 TRP D 379 HIS 0.012 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00446 (26212) covalent geometry : angle 0.66391 (35804) SS BOND : bond 0.00410 ( 18) SS BOND : angle 1.89455 ( 36) hydrogen bonds : bond 0.03776 ( 1037) hydrogen bonds : angle 4.26345 ( 2973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.59 seconds wall clock time: 89 minutes 11.95 seconds (5351.95 seconds total)