Starting phenix.real_space_refine on Mon Aug 25 00:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl6_40574/08_2025/8sl6_40574.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 15329 2.51 5 N 4219 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s 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: 23954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 5867 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 35, 'TRANS': 857} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1411 Unresolved non-hydrogen angles: 1771 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLU:plan': 41, 'ASN:plan1': 14, 'ARG:plan': 38, 'PHE:plan': 27, 'TRP:plan': 3, 'ASP:plan': 22, 'GLN:plan1': 20, 'HIS:plan': 8, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 834 Chain: "B" Number of atoms: 5976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 5976 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 363} Link IDs: {'PTRANS': 35, 'TRANS': 872} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1424 Unresolved non-hydrogen angles: 1789 Unresolved non-hydrogen dihedrals: 1181 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLU:plan': 44, 'ASN:plan1': 14, 'ARG:plan': 33, 'PHE:plan': 28, 'TRP:plan': 3, 'ASP:plan': 24, 'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 837 Chain: "C" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 6032 Classifications: {'peptide': 920} Incomplete info: {'truncation_to_alanine': 372} Link IDs: {'PTRANS': 35, 'TRANS': 884} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1455 Unresolved non-hydrogen angles: 1822 Unresolved non-hydrogen dihedrals: 1197 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLU:plan': 46, 'ASN:plan1': 14, 'ARG:plan': 39, 'PHE:plan': 26, 'TRP:plan': 2, 'ASP:plan': 24, 'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 849 Chain: "D" Number of atoms: 6079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 6079 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 353} Link IDs: {'PTRANS': 35, 'TRANS': 877} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1358 Unresolved non-hydrogen angles: 1710 Unresolved non-hydrogen dihedrals: 1116 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLU:plan': 42, 'ASN:plan1': 15, 'ARG:plan': 28, 'PHE:plan': 25, 'TRP:plan': 2, 'ASP:plan': 24, 'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 782 Time building chain proxies: 6.13, per 1000 atoms: 0.26 Number of scatterers: 23954 At special positions: 0 Unit cell: (150.12, 150.12, 167.4, 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 67 16.00 O 4339 8.00 N 4219 7.00 C 15329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6942 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 9 sheets defined 74.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.995A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.925A pdb=" N LEU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.695A pdb=" N ALA A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'A' and resid 347 through 362 removed outlier: 4.433A pdb=" N ALA A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.368A pdb=" N SER A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 394 Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.818A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.549A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.543A pdb=" N ALA A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 590 removed outlier: 4.020A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.534A pdb=" N VAL A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 removed outlier: 3.528A pdb=" N SER A 606 " --> pdb=" O HIS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.816A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.794A pdb=" N TRP A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 719 through 729 removed outlier: 3.577A pdb=" N ALA A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 756 Processing helix chain 'A' and resid 763 through 787 removed outlier: 3.610A pdb=" N GLU A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.007A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 825 Processing helix chain 'A' and resid 829 through 851 removed outlier: 4.334A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 895 removed outlier: 4.506A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.600A pdb=" N ARG A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 959 through 984 Processing helix chain 'A' and resid 984 through 1006 removed outlier: 4.148A pdb=" N ALA A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 993 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 removed outlier: 4.192A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.917A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.873A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 236 through 248 removed outlier: 4.100A pdb=" N LEU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 330 through 345 Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.597A pdb=" N ALA B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 393 Processing helix chain 'B' and resid 395 through 404 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.796A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.968A pdb=" N TYR B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 561 removed outlier: 3.794A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 574 through 591 Processing helix chain 'B' and resid 592 through 599 removed outlier: 3.854A pdb=" N VAL B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.526A pdb=" N LEU B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.534A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.749A pdb=" N GLN B 629 " --> pdb=" O HIS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 655 removed outlier: 3.875A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.619A pdb=" N ALA B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 756 removed outlier: 3.707A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 787 removed outlier: 3.698A pdb=" N GLU B 767 " --> pdb=" O PRO B 763 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 770 " --> pdb=" O SER B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 803 Processing helix chain 'B' and resid 804 through 824 removed outlier: 3.526A pdb=" N CYS B 823 " --> pdb=" O VAL B 819 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.920A pdb=" N HIS B 855 " --> pdb=" O PHE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 895 removed outlier: 3.742A pdb=" N ARG B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 removed outlier: 4.960A pdb=" N ARG B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 959 through 984 removed outlier: 3.589A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1006 removed outlier: 3.659A pdb=" N MET B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1027 Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1090 Processing helix chain 'B' and resid 1090 through 1095 Processing helix chain 'B' and resid 1097 through 1106 removed outlier: 4.354A pdb=" N ILE B1101 " --> pdb=" O GLN B1097 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B1102 " --> pdb=" O GLU B1098 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B1106 " --> pdb=" O LYS B1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 61 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.535A pdb=" N LEU C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.845A pdb=" N LEU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.633A pdb=" N ALA C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.625A pdb=" N ALA C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'C' and resid 347 through 360 removed outlier: 3.622A pdb=" N TYR C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 removed outlier: 3.868A pdb=" N ASN C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 5.068A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.657A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 429 through 446 removed outlier: 3.643A pdb=" N GLU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 478 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.981A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 543 through 559 removed outlier: 4.139A pdb=" N ALA C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 Processing helix chain 'C' and resid 574 through 591 removed outlier: 4.051A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 590 " --> pdb=" O CYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 600 removed outlier: 3.939A pdb=" N ALA C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 606 Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 removed outlier: 4.184A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 638 Processing helix chain 'C' and resid 645 through 653 Processing helix chain 'C' and resid 656 through 662 removed outlier: 3.983A pdb=" N TYR C 660 " --> pdb=" O PRO C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 729 removed outlier: 3.881A pdb=" N ALA C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 756 removed outlier: 3.817A pdb=" N VAL C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 787 Processing helix chain 'C' and resid 793 through 803 removed outlier: 3.605A pdb=" N LYS C 797 " --> pdb=" O ARG C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 removed outlier: 3.572A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 853 removed outlier: 4.038A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 848 " --> pdb=" O PHE C 844 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 849 " --> pdb=" O THR C 845 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 895 removed outlier: 4.234A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 866 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 917 removed outlier: 4.846A pdb=" N ARG C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 959 through 985 Processing helix chain 'C' and resid 987 through 1006 Processing helix chain 'C' and resid 1010 through 1027 removed outlier: 3.834A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1115 removed outlier: 3.767A pdb=" N LEU C1113 " --> pdb=" O ASN C1109 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU C1114 " --> pdb=" O TYR C1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.545A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.729A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.838A pdb=" N LEU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 241 " --> pdb=" O PRO D 237 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.566A pdb=" N ALA D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 295 through 310 Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.540A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 4.050A pdb=" N TYR D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 379 through 392 removed outlier: 4.378A pdb=" N VAL D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.729A pdb=" N LEU D 413 " --> pdb=" O MET D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 429 through 446 Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 527 removed outlier: 4.016A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 527 " --> pdb=" O TRP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.923A pdb=" N MET D 539 " --> pdb=" O TYR D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 561 removed outlier: 3.767A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 574 through 591 removed outlier: 4.073A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 590 " --> pdb=" O CYS D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 598 Processing helix chain 'D' and resid 610 through 618 Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.923A pdb=" N PHE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 624 " --> pdb=" O LYS D 620 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 625' Processing helix chain 'D' and resid 625 through 638 removed outlier: 3.545A pdb=" N GLN D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 719 through 729 Processing helix chain 'D' and resid 729 through 757 removed outlier: 4.262A pdb=" N LEU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 754 " --> pdb=" O TYR D 750 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 787 removed outlier: 3.638A pdb=" N THR D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 771 " --> pdb=" O GLU D 767 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE D 775 " --> pdb=" O TYR D 771 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR D 776 " --> pdb=" O PHE D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 803 Processing helix chain 'D' and resid 804 through 826 Processing helix chain 'D' and resid 830 through 851 removed outlier: 4.461A pdb=" N LEU D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR D 845 " --> pdb=" O PHE D 841 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 846 " --> pdb=" O MET D 842 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 847 " --> pdb=" O VAL D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 895 removed outlier: 4.129A pdb=" N ASP D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 895 " --> pdb=" O GLN D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 916 removed outlier: 3.570A pdb=" N ILE D 904 " --> pdb=" O ARG D 900 " (cutoff:3.500A) Proline residue: D 912 - end of helix removed outlier: 3.741A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 959 through 1006 removed outlier: 3.801A pdb=" N PHE D 981 " --> pdb=" O PHE D 977 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 984 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLY D 986 " --> pdb=" O GLN D 982 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 993 " --> pdb=" O ASP D 989 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 994 " --> pdb=" O MET D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1027 removed outlier: 4.396A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1108 removed outlier: 3.936A pdb=" N ALA D1108 " --> pdb=" O LEU D1104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 188 removed outlier: 5.753A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 103 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N MET A 139 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 105 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER A 141 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N SER A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 68 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 231 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 70 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 256 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR A 319 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 255 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 188 removed outlier: 6.736A pdb=" N ALA B 136 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 186 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 105 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N SER B 141 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 71 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 256 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP B 253 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR B 319 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 255 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 28 Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.964A pdb=" N ALA C 136 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE C 186 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 101 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 137 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE C 103 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET C 139 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 105 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N SER C 141 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 71 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER C 106 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 256 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 253 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TYR C 319 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 255 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 188 removed outlier: 6.929A pdb=" N ALA D 136 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE D 186 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE D 103 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N MET D 139 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 256 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 253 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N TYR D 319 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 255 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 601 through 602 removed outlier: 3.638A pdb=" N THR D 608 " --> pdb=" O ASN D 602 " (cutoff:3.500A) 1859 hydrogen bonds defined for protein. 5544 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: 4.88 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4015 1.32 - 1.44: 6511 1.44 - 1.57: 13829 1.57 - 1.69: 0 1.69 - 1.82: 96 Bond restraints: 24451 Sorted by residual: bond pdb=" CA TRP D 537 " pdb=" C TRP D 537 " ideal model delta sigma weight residual 1.522 1.434 0.088 1.40e-02 5.10e+03 3.99e+01 bond pdb=" C TYR D 910 " pdb=" O TYR D 910 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.28e+01 bond pdb=" C PHE D 536 " pdb=" N TRP D 537 " ideal model delta sigma weight residual 1.335 1.299 0.036 1.38e-02 5.25e+03 6.69e+00 bond pdb=" C GLY D 859 " pdb=" N PRO D 860 " ideal model delta sigma weight residual 1.336 1.314 0.022 9.80e-03 1.04e+04 5.06e+00 bond pdb=" CB TRP D 605 " pdb=" CG TRP D 605 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.07e+00 ... (remaining 24446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 32673 1.79 - 3.57: 829 3.57 - 5.36: 135 5.36 - 7.14: 28 7.14 - 8.93: 4 Bond angle restraints: 33669 Sorted by residual: angle pdb=" N LEU D 914 " pdb=" CA LEU D 914 " pdb=" C LEU D 914 " ideal model delta sigma weight residual 112.04 119.71 -7.67 1.44e+00 4.82e-01 2.83e+01 angle pdb=" C LEU D 914 " pdb=" N GLN D 915 " pdb=" CA GLN D 915 " ideal model delta sigma weight residual 120.29 112.76 7.53 1.42e+00 4.96e-01 2.81e+01 angle pdb=" CA ARG D 911 " pdb=" C ARG D 911 " pdb=" N PRO D 912 " ideal model delta sigma weight residual 120.77 116.47 4.30 9.70e-01 1.06e+00 1.97e+01 angle pdb=" N LEU D 901 " pdb=" CA LEU D 901 " pdb=" C LEU D 901 " ideal model delta sigma weight residual 111.14 115.51 -4.37 1.08e+00 8.57e-01 1.64e+01 angle pdb=" CA LEU D 914 " pdb=" C LEU D 914 " pdb=" O LEU D 914 " ideal model delta sigma weight residual 120.31 115.52 4.79 1.25e+00 6.40e-01 1.47e+01 ... (remaining 33664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13198 17.65 - 35.29: 762 35.29 - 52.94: 94 52.94 - 70.58: 12 70.58 - 88.22: 13 Dihedral angle restraints: 14079 sinusoidal: 3510 harmonic: 10569 Sorted by residual: dihedral pdb=" CA ALA D 348 " pdb=" C ALA D 348 " pdb=" N GLN D 349 " pdb=" CA GLN D 349 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE B 412 " pdb=" C PHE B 412 " pdb=" N LEU B 413 " pdb=" CA LEU B 413 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 856 " pdb=" C LYS A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3955 0.080 - 0.159: 212 0.159 - 0.239: 1 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 4169 Sorted by residual: chirality pdb=" CA LEU D 914 " pdb=" N LEU D 914 " pdb=" C LEU D 914 " pdb=" CB LEU D 914 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA TRP D 537 " pdb=" N TRP D 537 " pdb=" C TRP D 537 " pdb=" CB TRP D 537 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CG LEU C 522 " pdb=" CB LEU C 522 " pdb=" CD1 LEU C 522 " pdb=" CD2 LEU C 522 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 4166 not shown) Planarity restraints: 4347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 904 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ILE D 904 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE D 904 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D 905 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS D 655 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO D 656 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 656 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 656 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 176 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO C 177 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " 0.031 5.00e-02 4.00e+02 ... (remaining 4344 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 486 2.68 - 3.24: 27194 3.24 - 3.79: 38560 3.79 - 4.35: 43428 4.35 - 4.90: 69531 Nonbonded interactions: 179199 Sorted by model distance: nonbonded pdb=" NH1 ARG B 482 " pdb=" O GLY B 483 " model vdw 2.128 3.120 nonbonded pdb=" O PHE D 402 " pdb=" OG SER D 405 " model vdw 2.149 3.040 nonbonded pdb=" O PHE B 476 " pdb=" NZ LYS B 552 " model vdw 2.151 3.120 nonbonded pdb=" O SER B 426 " pdb=" OG SER B 429 " model vdw 2.153 3.040 nonbonded pdb=" O PHE A 746 " pdb=" OG SER A 749 " model vdw 2.161 3.040 ... (remaining 179194 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 24 through 376 or (resid 377 through 379 and (name N or na \ me CA or name C or name O or name CB )) or resid 380 through 382 or (resid 383 a \ nd (name N or name CA or name C or name O or name CB )) or resid 384 through 386 \ or (resid 387 and (name N or name CA or name C or name O or name CB )) or resid \ 388 or (resid 389 through 390 and (name N or name CA or name C or name O or nam \ e CB )) or resid 391 through 394 or (resid 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 or (resid 400 and (name N o \ r name CA or name C or name O or name CB )) or resid 401 through 403 or (resid 4 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 405 through \ 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 481 or (resid 482 and (name N or name CA or name C or name O or \ name CB )) or resid 483 through 514 or (resid 515 and (name N or name CA or nam \ e C or name O or name CB )) or resid 516 through 541 or (resid 542 and (name N o \ r name CA or name C or name O or name CB )) or resid 543 through 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) or r \ esid 602 through 607 or (resid 608 and (name N or name CA or name C or name O or \ name CB )) or resid 609 through 615 or (resid 616 through 621 and (name N or na \ me CA or name C or name O or name CB )) or resid 622 through 652 or (resid 653 t \ hrough 655 and (name N or name CA or name C or name O or name CB )) or resid 656 \ through 659 or (resid 660 through 720 and (name N or name CA or name C or name \ O or name CB )) or resid 721 through 769 or (resid 770 through 772 and (name N o \ r name CA or name C or name O or name CB )) or resid 773 through 873 or (resid 8 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 875 through \ 896 or (resid 898 and (name N or name CA or name C or name O or name CB )) or r \ esid 899 through 1089 or (resid 1090 through 1091 and (name N or name CA or name \ C or name O or name CB )) or resid 1092)) selection = (chain 'B' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or resid 347 through 360 or (resid 361 through 3 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 369 through \ 376 or (resid 377 through 379 and (name N or name CA or name C or name O or nam \ e CB )) or resid 380 through 382 or (resid 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 through 403 \ or (resid 404 and (name N or name CA or name C or name O or name CB )) or resid \ 405 through 408 or (resid 409 through 410 and (name N or name CA or name C or n \ ame O or name CB )) or resid 411 through 414 or (resid 415 and (name N or name C \ A or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or na \ me CA or name C or name O or name CB )) or resid 418 through 446 or (resid 464 a \ nd (name N or name CA or name C or name O or name CB )) or resid 465 through 481 \ or (resid 482 and (name N or name CA or name C or name O or name CB )) or resid \ 483 through 517 or (resid 518 and (name N or name CA or name C or name O or nam \ e CB )) or resid 519 through 538 or (resid 539 and (name N or name CA or name C \ or name O or name CB )) or resid 540 or (resid 541 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 through 555 or (resid 556 a \ nd (name N or name CA or name C or name O or name CB )) or resid 557 through 600 \ or (resid 601 and (name N or name CA or name C or name O or name CB )) or resid \ 602 through 606 or (resid 607 through 608 and (name N or name CA or name C or n \ ame O or name CB )) or resid 609 through 615 or (resid 616 through 621 and (name \ N or name CA or name C or name O or name CB )) or resid 622 through 652 or (res \ id 653 through 655 and (name N or name CA or name C or name O or name CB )) or r \ esid 656 through 659 or (resid 660 through 720 and (name N or name CA or name C \ or name O or name CB )) or resid 721 through 769 or (resid 770 through 772 and ( \ name N or name CA or name C or name O or name CB )) or resid 773 through 846 or \ (resid 847 through 854 and (name N or name CA or name C or name O or name CB )) \ or resid 855 through 1082 or (resid 1083 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1084 through 1086 or (resid 1087 through 1091 and (na \ me N or name CA or name C or name O or name CB )) or resid 1092)) selection = (chain 'C' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 through 360 or (resid 361 through 368 a \ nd (name N or name CA or name C or name O or name CB )) or resid 369 through 377 \ or (resid 378 through 379 and (name N or name CA or name C or name O or name CB \ )) or resid 380 through 382 or (resid 383 and (name N or name CA or name C or n \ ame O or name CB )) or resid 384 through 386 or (resid 387 and (name N or name C \ A or name C or name O or name CB )) or resid 388 or (resid 389 through 390 and ( \ name N or name CA or name C or name O or name CB )) or resid 391 through 393 or \ (resid 394 through 395 and (name N or name CA or name C or name O or name CB )) \ or resid 396 through 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 or (resid 400 and (name N or name CA or name C or n \ ame O or name CB )) or resid 401 through 408 or (resid 409 through 410 and (name \ N or name CA or name C or name O or name CB )) or resid 411 through 414 or (res \ id 415 and (name N or name CA or name C or name O or name CB )) or resid 416 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 446 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 514 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 517 or (resid 518 and (name \ N or name CA or name C or name O or name CB )) or resid 519 through 526 or (res \ id 527 and (name N or name CA or name C or name O or name CB )) or resid 528 thr \ ough 652 or (resid 653 through 655 and (name N or name CA or name C or name O or \ name CB )) or resid 656 through 659 or (resid 660 through 720 and (name N or na \ me CA or name C or name O or name CB )) or resid 721 through 769 or (resid 770 t \ hrough 772 and (name N or name CA or name C or name O or name CB )) or resid 773 \ through 846 or (resid 847 through 854 and (name N or name CA or name C or name \ O or name CB )) or resid 855 through 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 through 1077 or (resid 1078 through \ 1079 and (name N or name CA or name C or name O or name CB )) or resid 1080 thr \ ough 1089 or (resid 1090 through 1091 and (name N or name CA or name C or name O \ or name CB )) or resid 1092)) selection = (chain 'D' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or resid 347 through 360 or (resid 361 through 3 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 369 through \ 376 or (resid 377 through 379 and (name N or name CA or name C or name O or nam \ e CB )) or resid 380 through 397 or (resid 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 or (resid 400 and (name N or name CA or nam \ e C or name O or name CB )) or resid 401 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 408 or (resid 4 \ 09 through 410 and (name N or name CA or name C or name O or name CB )) or resid \ 411 through 414 or (resid 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or \ name CB )) or resid 418 through 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 446 or (resid 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 481 or (resid 4 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 483 through \ 484 or resid 509 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 516 through 517 or (resid 518 and (name N or name \ CA or name C or name O or name CB )) or resid 519 through 526 or (resid 527 and \ (name N or name CA or name C or name O or name CB )) or resid 528 or (resid 529 \ and (name N or name CA or name C or name O or name CB )) or resid 530 through 53 \ 8 or (resid 539 and (name N or name CA or name C or name O or name CB )) or (res \ id 540 through 542 and (name N or name CA or name C or name O or name CB )) or r \ esid 543 through 554 or (resid 555 through 556 and (name N or name CA or name C \ or name O or name CB )) or resid 557 through 584 or (resid 585 and (name N or na \ me CA or name C or name O or name CB )) or resid 586 through 592 or (resid 593 t \ hrough 594 and (name N or name CA or name C or name O or name CB )) or resid 595 \ through 599 or (resid 600 through 601 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 606 or (resid 607 through 608 and (name N o \ r name CA or name C or name O or name CB )) or resid 609 through 615 or (resid 6 \ 16 through 621 and (name N or name CA or name C or name O or name CB )) or resid \ 622 through 721 or (resid 722 and (name N or name CA or name C or name O or nam \ e CB )) or resid 723 through 816 or (resid 817 and (name N or name CA or name C \ or name O or name CB )) or resid 818 through 830 or (resid 831 through 832 and ( \ name N or name CA or name C or name O or name CB )) or resid 833 through 843 or \ (resid 844 and (name N or name CA or name C or name O or name CB )) or resid 845 \ through 846 or (resid 847 through 854 and (name N or name CA or name C or name \ O or name CB )) or resid 855 through 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 through 1082 or (resid 1083 and (na \ me N or name CA or name C or name O or name CB )) or resid 1084 through 1089 or \ (resid 1090 through 1091 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1092)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.870 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.005 0.088 24451 Z= 0.278 Angle : 0.710 8.928 33669 Z= 0.428 Chirality : 0.039 0.398 4169 Planarity : 0.004 0.065 4347 Dihedral : 11.903 88.225 7137 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 3522 helix: -0.37 (0.09), residues: 2441 sheet: -0.61 (0.33), residues: 208 loop : -2.24 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 518 TYR 0.018 0.002 TYR D 535 PHE 0.029 0.002 PHE C 476 TRP 0.035 0.002 TRP C 302 HIS 0.010 0.001 HIS C 998 Details of bonding type rmsd covalent geometry : bond 0.00538 (24451) covalent geometry : angle 0.70950 (33669) hydrogen bonds : bond 0.14136 ( 1859) hydrogen bonds : angle 6.21179 ( 5544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8905 (tp) cc_final: 0.8527 (pp) REVERT: A 752 LEU cc_start: 0.9152 (tp) cc_final: 0.8890 (pp) REVERT: B 243 MET cc_start: 0.8916 (tmm) cc_final: 0.8566 (tmm) REVERT: B 254 LEU cc_start: 0.9181 (tp) cc_final: 0.8464 (pp) REVERT: B 882 TRP cc_start: 0.9029 (t-100) cc_final: 0.8807 (t-100) REVERT: B 1000 ILE cc_start: 0.9723 (mt) cc_final: 0.9427 (tt) REVERT: C 135 VAL cc_start: 0.9255 (m) cc_final: 0.9000 (p) REVERT: C 806 TRP cc_start: 0.8542 (m100) cc_final: 0.8108 (m100) REVERT: C 972 LEU cc_start: 0.9279 (mm) cc_final: 0.8979 (pp) REVERT: D 232 LEU cc_start: 0.8987 (tp) cc_final: 0.8778 (tt) REVERT: D 882 TRP cc_start: 0.8867 (t-100) cc_final: 0.8560 (t-100) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1339 time to fit residues: 53.6806 Evaluate side-chains 182 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 118 GLN B 123 HIS B 204 GLN B 602 ASN B 603 HIS B1060 ASN C 123 HIS C 204 GLN C 394 ASN C 439 HIS C 528 ASN C 603 HIS C 737 ASN C1060 ASN D 184 HIS D 344 HIS D 528 ASN D 998 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.081281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062915 restraints weight = 161599.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060985 restraints weight = 118872.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061181 restraints weight = 119186.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061437 restraints weight = 90336.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061513 restraints weight = 84463.043| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24451 Z= 0.141 Angle : 0.541 6.666 33669 Z= 0.290 Chirality : 0.037 0.140 4169 Planarity : 0.004 0.053 4347 Dihedral : 4.197 21.570 3703 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.23 % Allowed : 4.83 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3522 helix: 1.41 (0.10), residues: 2521 sheet: 0.09 (0.34), residues: 198 loop : -1.91 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 286 TYR 0.014 0.001 TYR D 535 PHE 0.030 0.001 PHE A1061 TRP 0.023 0.001 TRP B 253 HIS 0.007 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00281 (24451) covalent geometry : angle 0.54075 (33669) hydrogen bonds : bond 0.04361 ( 1859) hydrogen bonds : angle 4.37758 ( 5544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.7717 (mtt) cc_final: 0.7488 (mtt) REVERT: A 752 LEU cc_start: 0.9139 (tp) cc_final: 0.8845 (pp) REVERT: A 999 LEU cc_start: 0.9201 (tp) cc_final: 0.9000 (tp) REVERT: B 557 MET cc_start: 0.8792 (tmm) cc_final: 0.8522 (tmm) REVERT: B 581 ASP cc_start: 0.8648 (m-30) cc_final: 0.8367 (m-30) REVERT: C 387 MET cc_start: 0.8572 (tmm) cc_final: 0.8227 (tmm) REVERT: C 395 LYS cc_start: 0.9022 (mttt) cc_final: 0.8533 (mmmm) REVERT: C 581 ASP cc_start: 0.8404 (m-30) cc_final: 0.8202 (m-30) REVERT: C 972 LEU cc_start: 0.9415 (mm) cc_final: 0.9088 (pp) REVERT: D 421 LEU cc_start: 0.9463 (mt) cc_final: 0.9261 (tp) REVERT: D 539 MET cc_start: 0.8852 (mtm) cc_final: 0.8424 (mtt) REVERT: D 882 TRP cc_start: 0.9022 (t-100) cc_final: 0.8512 (t60) outliers start: 4 outliers final: 1 residues processed: 235 average time/residue: 0.1259 time to fit residues: 51.3718 Evaluate side-chains 181 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 349 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 276 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 109 optimal weight: 20.0000 chunk 309 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 315 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 225 GLN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 HIS B 612 HIS C 528 ASN C 998 HIS D 419 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060332 restraints weight = 164479.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.057952 restraints weight = 135549.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058017 restraints weight = 145638.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058053 restraints weight = 105492.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058320 restraints weight = 101976.180| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 24451 Z= 0.389 Angle : 0.772 11.480 33669 Z= 0.425 Chirality : 0.042 0.175 4169 Planarity : 0.006 0.057 4347 Dihedral : 4.910 23.566 3703 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.29 % Allowed : 7.19 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3522 helix: 0.71 (0.10), residues: 2509 sheet: -0.06 (0.34), residues: 211 loop : -2.01 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 518 TYR 0.023 0.003 TYR A 535 PHE 0.028 0.003 PHE D 994 TRP 0.047 0.003 TRP D 302 HIS 0.013 0.002 HIS D 998 Details of bonding type rmsd covalent geometry : bond 0.00786 (24451) covalent geometry : angle 0.77226 (33669) hydrogen bonds : bond 0.05677 ( 1859) hydrogen bonds : angle 5.38812 ( 5544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 ASP cc_start: 0.8930 (t0) cc_final: 0.8590 (m-30) REVERT: C 806 TRP cc_start: 0.8316 (m100) cc_final: 0.7940 (m100) REVERT: C 972 LEU cc_start: 0.9408 (mm) cc_final: 0.9146 (pp) REVERT: D 355 LEU cc_start: 0.9553 (tt) cc_final: 0.9352 (tt) REVERT: D 882 TRP cc_start: 0.8962 (t-100) cc_final: 0.8611 (t-100) outliers start: 5 outliers final: 3 residues processed: 201 average time/residue: 0.1302 time to fit residues: 45.4828 Evaluate side-chains 163 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 255 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 349 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN C 528 ASN D 419 GLN ** D 420 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 = 0.3695 r_free = 0.3695 target = 0.079510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061756 restraints weight = 163519.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059786 restraints weight = 124269.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059764 restraints weight = 139294.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.060078 restraints weight = 102440.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060126 restraints weight = 95099.028| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24451 Z= 0.217 Angle : 0.571 6.718 33669 Z= 0.312 Chirality : 0.038 0.169 4169 Planarity : 0.004 0.052 4347 Dihedral : 4.398 21.416 3703 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3522 helix: 1.46 (0.10), residues: 2510 sheet: 0.02 (0.35), residues: 199 loop : -1.77 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 518 TYR 0.019 0.002 TYR D 535 PHE 0.021 0.002 PHE A 748 TRP 0.054 0.002 TRP A 302 HIS 0.008 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00441 (24451) covalent geometry : angle 0.57096 (33669) hydrogen bonds : bond 0.04327 ( 1859) hydrogen bonds : angle 4.54819 ( 5544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8535 (tp-100) REVERT: B 610 CYS cc_start: 0.8960 (m) cc_final: 0.8753 (m) REVERT: C 806 TRP cc_start: 0.8307 (m100) cc_final: 0.7929 (m100) REVERT: C 972 LEU cc_start: 0.9399 (mm) cc_final: 0.9133 (pp) REVERT: D 539 MET cc_start: 0.8736 (mtm) cc_final: 0.8439 (mtm) REVERT: D 882 TRP cc_start: 0.9001 (t-100) cc_final: 0.8548 (t-100) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.1263 time to fit residues: 45.3101 Evaluate side-chains 167 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 102 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 98 optimal weight: 0.0060 chunk 193 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 290 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 528 ASN ** D 420 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 = 0.3680 r_free = 0.3680 target = 0.078821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061032 restraints weight = 162920.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058841 restraints weight = 128000.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059098 restraints weight = 128589.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059101 restraints weight = 97689.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059301 restraints weight = 94281.612| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24451 Z= 0.246 Angle : 0.605 8.924 33669 Z= 0.328 Chirality : 0.038 0.170 4169 Planarity : 0.005 0.053 4347 Dihedral : 4.406 20.806 3703 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3522 helix: 1.48 (0.10), residues: 2511 sheet: -0.09 (0.34), residues: 211 loop : -1.81 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 518 TYR 0.019 0.002 TYR D 535 PHE 0.044 0.002 PHE D 748 TRP 0.028 0.002 TRP D 302 HIS 0.008 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00500 (24451) covalent geometry : angle 0.60541 (33669) hydrogen bonds : bond 0.04491 ( 1859) hydrogen bonds : angle 4.61514 ( 5544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.9053 (tp) cc_final: 0.8845 (tp) REVERT: A 840 ASP cc_start: 0.8881 (t0) cc_final: 0.8545 (m-30) REVERT: C 581 ASP cc_start: 0.8379 (m-30) cc_final: 0.8126 (m-30) REVERT: C 806 TRP cc_start: 0.8292 (m100) cc_final: 0.7952 (m100) REVERT: C 972 LEU cc_start: 0.9381 (mm) cc_final: 0.9060 (pp) REVERT: D 882 TRP cc_start: 0.8916 (t-100) cc_final: 0.8535 (t-100) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1197 time to fit residues: 41.2057 Evaluate side-chains 165 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 66 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 221 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 355 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 345 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN C 528 ASN C 998 HIS ** D 420 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 = 0.3693 r_free = 0.3693 target = 0.079410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061632 restraints weight = 163340.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059630 restraints weight = 118868.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059918 restraints weight = 135302.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059527 restraints weight = 116799.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059820 restraints weight = 100309.063| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24451 Z= 0.203 Angle : 0.567 13.525 33669 Z= 0.306 Chirality : 0.037 0.153 4169 Planarity : 0.005 0.146 4347 Dihedral : 4.280 25.443 3703 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3522 helix: 1.70 (0.10), residues: 2522 sheet: -0.18 (0.34), residues: 211 loop : -1.86 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 529 TYR 0.016 0.002 TYR D 535 PHE 0.030 0.002 PHE C 476 TRP 0.021 0.002 TRP D 302 HIS 0.007 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00415 (24451) covalent geometry : angle 0.56730 (33669) hydrogen bonds : bond 0.04135 ( 1859) hydrogen bonds : angle 4.42425 ( 5544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8602 (tmm) cc_final: 0.8173 (tmm) REVERT: A 995 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8315 (tp-100) REVERT: B 243 MET cc_start: 0.9184 (mmp) cc_final: 0.8904 (mmp) REVERT: C 581 ASP cc_start: 0.8368 (m-30) cc_final: 0.8103 (m-30) REVERT: C 806 TRP cc_start: 0.8329 (m100) cc_final: 0.7983 (m100) REVERT: C 972 LEU cc_start: 0.9354 (mm) cc_final: 0.9080 (pp) REVERT: D 413 LEU cc_start: 0.8528 (tp) cc_final: 0.8150 (tt) REVERT: D 882 TRP cc_start: 0.8918 (t-100) cc_final: 0.8515 (t-100) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1274 time to fit residues: 42.9977 Evaluate side-chains 164 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 305 optimal weight: 0.1980 chunk 38 optimal weight: 20.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 528 ASN C 998 HIS ** D 420 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 = 0.3725 r_free = 0.3725 target = 0.080914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062706 restraints weight = 161672.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.061240 restraints weight = 109837.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061548 restraints weight = 107571.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061775 restraints weight = 82228.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061887 restraints weight = 75579.030| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24451 Z= 0.120 Angle : 0.502 7.615 33669 Z= 0.266 Chirality : 0.036 0.138 4169 Planarity : 0.004 0.064 4347 Dihedral : 3.958 19.087 3703 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.06 % Allowed : 1.78 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.15), residues: 3522 helix: 2.06 (0.10), residues: 2527 sheet: -0.03 (0.36), residues: 198 loop : -1.78 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 400 TYR 0.014 0.001 TYR C 422 PHE 0.029 0.001 PHE C 994 TRP 0.065 0.002 TRP B 302 HIS 0.006 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00250 (24451) covalent geometry : angle 0.50230 (33669) hydrogen bonds : bond 0.03639 ( 1859) hydrogen bonds : angle 3.99213 ( 5544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8764 (tmm) cc_final: 0.8433 (tmm) REVERT: A 387 MET cc_start: 0.7304 (mtt) cc_final: 0.6986 (mtt) REVERT: B 67 LEU cc_start: 0.9045 (pt) cc_final: 0.8823 (tt) REVERT: B 243 MET cc_start: 0.9108 (mmp) cc_final: 0.8900 (mmp) REVERT: B 610 CYS cc_start: 0.8772 (m) cc_final: 0.8570 (m) REVERT: C 581 ASP cc_start: 0.8322 (m-30) cc_final: 0.8068 (m-30) REVERT: C 806 TRP cc_start: 0.8103 (m100) cc_final: 0.7733 (m100) REVERT: C 972 LEU cc_start: 0.9224 (mm) cc_final: 0.8985 (pp) REVERT: D 243 MET cc_start: 0.9100 (ttm) cc_final: 0.8344 (tpp) REVERT: D 882 TRP cc_start: 0.8783 (t-100) cc_final: 0.8394 (t-100) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.1209 time to fit residues: 44.1053 Evaluate side-chains 171 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 271 optimal weight: 50.0000 chunk 109 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 183 optimal weight: 0.0370 chunk 71 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 196 optimal weight: 0.1980 chunk 55 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 overall best weight: 4.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.079135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061262 restraints weight = 162623.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059105 restraints weight = 119115.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059339 restraints weight = 137046.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059239 restraints weight = 110068.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059739 restraints weight = 94519.852| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24451 Z= 0.218 Angle : 0.587 14.874 33669 Z= 0.315 Chirality : 0.038 0.150 4169 Planarity : 0.004 0.079 4347 Dihedral : 4.157 20.375 3703 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.15), residues: 3522 helix: 1.85 (0.10), residues: 2531 sheet: -0.25 (0.34), residues: 208 loop : -1.74 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 518 TYR 0.020 0.002 TYR D 535 PHE 0.022 0.002 PHE A 476 TRP 0.066 0.002 TRP A 302 HIS 0.006 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00446 (24451) covalent geometry : angle 0.58652 (33669) hydrogen bonds : bond 0.04114 ( 1859) hydrogen bonds : angle 4.36666 ( 5544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9349 (tp) cc_final: 0.9147 (tp) REVERT: A 243 MET cc_start: 0.8747 (tmm) cc_final: 0.8439 (tmm) REVERT: A 254 LEU cc_start: 0.8980 (tp) cc_final: 0.8766 (tp) REVERT: A 999 LEU cc_start: 0.8820 (mm) cc_final: 0.8610 (mm) REVERT: B 243 MET cc_start: 0.9191 (mmp) cc_final: 0.8969 (mmp) REVERT: C 581 ASP cc_start: 0.8501 (m-30) cc_final: 0.8208 (m-30) REVERT: C 806 TRP cc_start: 0.8330 (m100) cc_final: 0.7981 (m100) REVERT: C 845 THR cc_start: 0.9366 (t) cc_final: 0.9141 (t) REVERT: C 972 LEU cc_start: 0.9289 (mm) cc_final: 0.9049 (pp) REVERT: D 413 LEU cc_start: 0.8528 (tp) cc_final: 0.8210 (tt) REVERT: D 882 TRP cc_start: 0.8949 (t-100) cc_final: 0.8509 (t-100) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1243 time to fit residues: 41.8173 Evaluate side-chains 162 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 56 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 349 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 112 optimal weight: 0.0060 chunk 51 optimal weight: 3.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061688 restraints weight = 162665.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059653 restraints weight = 116810.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059847 restraints weight = 125067.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060149 restraints weight = 93668.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060224 restraints weight = 86842.416| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24451 Z= 0.176 Angle : 0.541 7.221 33669 Z= 0.291 Chirality : 0.037 0.179 4169 Planarity : 0.004 0.063 4347 Dihedral : 4.056 18.164 3703 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3522 helix: 1.97 (0.10), residues: 2531 sheet: -0.28 (0.36), residues: 196 loop : -1.70 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 518 TYR 0.019 0.002 TYR B 164 PHE 0.027 0.001 PHE A1061 TRP 0.072 0.002 TRP D 302 HIS 0.009 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00366 (24451) covalent geometry : angle 0.54123 (33669) hydrogen bonds : bond 0.03867 ( 1859) hydrogen bonds : angle 4.21025 ( 5544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8791 (tmm) cc_final: 0.8488 (tmm) REVERT: B 243 MET cc_start: 0.9229 (mmp) cc_final: 0.8996 (mmp) REVERT: C 581 ASP cc_start: 0.8422 (m-30) cc_final: 0.8178 (m-30) REVERT: C 806 TRP cc_start: 0.8334 (m100) cc_final: 0.7973 (m100) REVERT: C 845 THR cc_start: 0.9356 (t) cc_final: 0.9107 (t) REVERT: C 972 LEU cc_start: 0.9282 (mm) cc_final: 0.9049 (pp) REVERT: D 243 MET cc_start: 0.9261 (ttm) cc_final: 0.8595 (tpp) REVERT: D 413 LEU cc_start: 0.8572 (tp) cc_final: 0.8279 (tt) REVERT: D 882 TRP cc_start: 0.8930 (t-100) cc_final: 0.8482 (t-100) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1119 time to fit residues: 37.8087 Evaluate side-chains 162 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 222 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 260 optimal weight: 0.5980 chunk 163 optimal weight: 40.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062919 restraints weight = 162326.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060884 restraints weight = 116462.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061391 restraints weight = 129479.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.061138 restraints weight = 102240.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061426 restraints weight = 93207.344| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24451 Z= 0.121 Angle : 0.509 7.074 33669 Z= 0.268 Chirality : 0.036 0.160 4169 Planarity : 0.004 0.050 4347 Dihedral : 3.834 18.667 3703 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.15), residues: 3522 helix: 2.17 (0.10), residues: 2538 sheet: -0.21 (0.36), residues: 199 loop : -1.65 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 518 TYR 0.019 0.001 TYR A 164 PHE 0.030 0.001 PHE A1061 TRP 0.063 0.002 TRP D 302 HIS 0.005 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00252 (24451) covalent geometry : angle 0.50853 (33669) hydrogen bonds : bond 0.03504 ( 1859) hydrogen bonds : angle 3.95235 ( 5544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9331 (tp) cc_final: 0.9129 (tp) REVERT: A 243 MET cc_start: 0.8768 (tmm) cc_final: 0.8465 (tmm) REVERT: B 243 MET cc_start: 0.9232 (mmp) cc_final: 0.9002 (mmp) REVERT: C 806 TRP cc_start: 0.8253 (m100) cc_final: 0.7863 (m100) REVERT: C 972 LEU cc_start: 0.9254 (mm) cc_final: 0.9017 (pp) REVERT: D 243 MET cc_start: 0.9243 (ttm) cc_final: 0.8599 (tpp) REVERT: D 882 TRP cc_start: 0.8893 (t-100) cc_final: 0.8422 (t60) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1155 time to fit residues: 41.4726 Evaluate side-chains 163 residues out of total 3182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 94 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 232 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.079613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061976 restraints weight = 162672.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059763 restraints weight = 121824.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060094 restraints weight = 128457.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060354 restraints weight = 93655.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060444 restraints weight = 90158.058| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24451 Z= 0.186 Angle : 0.557 7.373 33669 Z= 0.297 Chirality : 0.037 0.146 4169 Planarity : 0.004 0.066 4347 Dihedral : 3.998 18.044 3703 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.15), residues: 3522 helix: 2.01 (0.10), residues: 2528 sheet: -0.45 (0.35), residues: 199 loop : -1.63 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 518 TYR 0.021 0.002 TYR A 164 PHE 0.026 0.002 PHE A1061 TRP 0.058 0.002 TRP D 302 HIS 0.006 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00382 (24451) covalent geometry : angle 0.55682 (33669) hydrogen bonds : bond 0.03888 ( 1859) hydrogen bonds : angle 4.19102 ( 5544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.54 seconds wall clock time: 62 minutes 29.40 seconds (3749.40 seconds total)