Starting phenix.real_space_refine on Sat Aug 8 14:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.cif Found real_map, /net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.map" model { file = "/net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20yy_67423/08_2026/20yy_67423.cif" } resolution = 2.57 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= 0.003 sd= 0.019 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: 5 Type Number sf(0) Gaussians S 81 5.16 5 Cl 9 4.86 5 C 18042 2.51 5 N 4872 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 970} Chain: "B" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 970} Chain: "C" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 970} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "E" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 656 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain breaks: 1 Chain: "H" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 656 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain breaks: 1 Chain: "I" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 656 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.22 Number of scatterers: 28038 At special positions: 0 Unit cell: (138.6, 143.64, 156.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 9 17.00 S 81 16.00 O 5034 8.00 N 4872 7.00 C 18042 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 43 sheets defined 51.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 12 through 32 removed outlier: 4.107A pdb=" N SER A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 105 through 120 removed outlier: 3.586A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 170 removed outlier: 3.784A pdb=" N ARG A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.899A pdb=" N LEU A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.663A pdb=" N LEU A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.673A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.961A pdb=" N GLN A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 356 Processing helix chain 'A' and resid 356 through 381 removed outlier: 4.162A pdb=" N VAL A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 386 through 418 removed outlier: 4.586A pdb=" N GLY A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.903A pdb=" N SER A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.858A pdb=" N THR A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.576A pdb=" N THR A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 481 removed outlier: 4.211A pdb=" N PHE A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 530 through 549 removed outlier: 3.673A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.666A pdb=" N THR A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.818A pdb=" N GLU A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 773 through 777 removed outlier: 3.558A pdb=" N LEU A 777 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 824 through 833 removed outlier: 3.616A pdb=" N LEU A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 852 through 867 removed outlier: 4.109A pdb=" N GLU A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 886 through 896 removed outlier: 3.546A pdb=" N THR A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.507A pdb=" N VAL A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 948 removed outlier: 3.600A pdb=" N GLY A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 961 removed outlier: 3.549A pdb=" N THR A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 960 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 976 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.958A pdb=" N ARG A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1006 removed outlier: 3.654A pdb=" N VAL A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.632A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.794A pdb=" N SER B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.767A pdb=" N LEU B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 171 removed outlier: 3.567A pdb=" N ARG B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.576A pdb=" N LEU B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.565A pdb=" N LEU B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 294 through 311 removed outlier: 3.745A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 356 Processing helix chain 'B' and resid 356 through 381 removed outlier: 3.855A pdb=" N VAL B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 386 through 418 removed outlier: 3.727A pdb=" N LEU B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 426 through 433 removed outlier: 4.316A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA B 433 " --> pdb=" O TRP B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 455 through 461 removed outlier: 3.537A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 481 removed outlier: 4.106A pdb=" N PHE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 530 through 548 removed outlier: 3.566A pdb=" N LEU B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 576 through 590 Processing helix chain 'B' and resid 633 through 649 removed outlier: 3.806A pdb=" N GLU B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 639 " --> pdb=" O GLU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.604A pdb=" N GLU B 697 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 730 through 743 Processing helix chain 'B' and resid 770 through 777 removed outlier: 3.624A pdb=" N LEU B 773 " --> pdb=" O ASP B 770 " (cutoff:3.500A) Proline residue: B 775 - end of helix Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 824 through 833 removed outlier: 3.544A pdb=" N GLN B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 854 through 867 removed outlier: 3.725A pdb=" N ALA B 867 " --> pdb=" O SER B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 885 Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.569A pdb=" N THR B 896 " --> pdb=" O MET B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 899 No H-bonds generated for 'chain 'B' and resid 897 through 899' Processing helix chain 'B' and resid 900 through 911 Processing helix chain 'B' and resid 916 through 948 Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 962 through 976 removed outlier: 3.656A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.917A pdb=" N ARG B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1017 removed outlier: 4.205A pdb=" N LEU B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) Proline residue: B1009 - end of helix Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 12 through 33 removed outlier: 3.994A pdb=" N SER C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 105 through 120 removed outlier: 3.523A pdb=" N LEU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 124 removed outlier: 3.609A pdb=" N LEU C 124 " --> pdb=" O ARG C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 124' Processing helix chain 'C' and resid 153 through 170 removed outlier: 3.647A pdb=" N ARG C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.792A pdb=" N LEU C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 removed outlier: 3.725A pdb=" N ILE C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.562A pdb=" N GLN C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 356 Processing helix chain 'C' and resid 356 through 381 removed outlier: 3.831A pdb=" N VAL C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 363 " --> pdb=" O THR C 359 " (cutoff:3.500A) Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 386 through 396 Processing helix chain 'C' and resid 396 through 418 removed outlier: 3.706A pdb=" N GLY C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 426 through 433 removed outlier: 4.282A pdb=" N THR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 433 " --> pdb=" O TRP C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 447 through 452 Processing helix chain 'C' and resid 455 through 461 Processing helix chain 'C' and resid 461 through 481 removed outlier: 4.022A pdb=" N PHE C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 466 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 514 through 530 Processing helix chain 'C' and resid 530 through 548 removed outlier: 3.741A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 551 No H-bonds generated for 'chain 'C' and resid 549 through 551' Processing helix chain 'C' and resid 576 through 592 Processing helix chain 'C' and resid 633 through 649 removed outlier: 3.721A pdb=" N GLU C 638 " --> pdb=" O LEU C 634 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 696 Processing helix chain 'C' and resid 720 through 728 removed outlier: 3.636A pdb=" N ALA C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 743 Processing helix chain 'C' and resid 764 through 769 removed outlier: 3.679A pdb=" N ARG C 769 " --> pdb=" O GLU C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 777 Proline residue: C 775 - end of helix Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 824 through 836 Proline residue: C 834 - end of helix Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.616A pdb=" N ARG C 840 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 867 removed outlier: 3.547A pdb=" N SER C 864 " --> pdb=" O LYS C 860 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 896 removed outlier: 3.728A pdb=" N THR C 896 " --> pdb=" O MET C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 911 removed outlier: 3.571A pdb=" N PHE C 907 " --> pdb=" O GLY C 903 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 911 " --> pdb=" O PHE C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 948 removed outlier: 3.504A pdb=" N GLY C 922 " --> pdb=" O VAL C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 961 removed outlier: 3.584A pdb=" N THR C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 960 " --> pdb=" O ILE C 956 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 961 " --> pdb=" O GLU C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 981 removed outlier: 3.882A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Proline residue: C 979 - end of helix Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.789A pdb=" N VAL C1002 " --> pdb=" O ILE C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1017 removed outlier: 3.607A pdb=" N ALA C1010 " --> pdb=" O LEU C1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.604A pdb=" N VAL E 324 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 325 " --> pdb=" O VAL E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 325' Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 267 through 271 Processing helix chain 'G' and resid 321 through 325 Processing helix chain 'H' and resid 267 through 271 Processing helix chain 'H' and resid 321 through 325 removed outlier: 3.503A pdb=" N VAL H 324 " --> pdb=" O GLY H 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 271 Processing helix chain 'I' and resid 321 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 134 removed outlier: 5.590A pdb=" N GLY A 130 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN A 52 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A 86 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 92 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 84 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 94 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 82 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET A 96 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 180 removed outlier: 3.681A pdb=" N LYS A 176 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 143 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 144 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.557A pdb=" N ILE A 187 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 234 removed outlier: 4.609A pdb=" N ILE C 719 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 247 through 250 Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.869A pdb=" N ASN A 599 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 706 removed outlier: 4.055A pdb=" N VAL A 704 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 816 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 706 " --> pdb=" O THR A 814 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 814 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 793 through 801 removed outlier: 6.997A pdb=" N SER B 234 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 717 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 134 removed outlier: 5.532A pdb=" N GLY B 130 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASN B 52 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 81 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 180 removed outlier: 3.795A pdb=" N LYS B 176 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 143 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 144 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.664A pdb=" N ILE B 187 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 759 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 748 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 761 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N HIS B 746 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AB6, first strand: chain 'B' and resid 247 through 250 Processing sheet with id=AB7, first strand: chain 'B' and resid 274 through 277 removed outlier: 3.556A pdb=" N VAL B 604 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 630 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR B 600 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 628 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA B 602 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN B 626 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 604 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 624 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 702 through 706 removed outlier: 4.100A pdb=" N VAL B 704 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG B 816 " --> pdb=" O VAL B 704 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 706 " --> pdb=" O THR B 814 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B 814 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 672 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B 673 " --> pdb=" O GLY B 852 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 793 through 801 removed outlier: 6.950A pdb=" N SER C 234 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU B 717 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 129 through 134 removed outlier: 5.393A pdb=" N GLY C 130 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN C 52 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER C 86 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN C 92 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER C 84 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 94 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE C 82 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET C 96 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 174 through 180 removed outlier: 4.024A pdb=" N LYS C 176 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 143 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET C 289 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR C 141 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY C 142 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 324 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 144 " --> pdb=" O VAL C 322 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 266 removed outlier: 6.502A pdb=" N ILE C 187 " --> pdb=" O LEU C 760 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 748 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 761 " --> pdb=" O HIS C 746 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS C 746 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AC5, first strand: chain 'C' and resid 247 through 250 removed outlier: 4.001A pdb=" N ARG C 253 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 274 through 277 removed outlier: 6.808A pdb=" N LEU C 630 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR C 600 " --> pdb=" O VAL C 628 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 628 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA C 602 " --> pdb=" O GLN C 626 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN C 626 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL C 604 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE C 624 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 706 removed outlier: 4.128A pdb=" N VAL C 704 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG C 816 " --> pdb=" O VAL C 704 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU C 706 " --> pdb=" O THR C 814 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C 814 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 672 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN C 673 " --> pdb=" O GLY C 852 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 317 through 320 removed outlier: 7.751A pdb=" N ILE D 15 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG D 12 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 334 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA D 14 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.222A pdb=" N LEU D 264 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG D 296 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 272 through 274 Processing sheet with id=AD2, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.036A pdb=" N ALA E 14 " --> pdb=" O ILE E 334 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 264 through 267 removed outlier: 4.125A pdb=" N LEU E 264 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AD5, first strand: chain 'F' and resid 317 through 318 Processing sheet with id=AD6, first strand: chain 'F' and resid 264 through 267 removed outlier: 4.115A pdb=" N LEU F 264 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 272 through 273 removed outlier: 3.730A pdb=" N THR F 289 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 317 through 318 Processing sheet with id=AD9, first strand: chain 'G' and resid 272 through 274 removed outlier: 3.943A pdb=" N THR G 289 " --> pdb=" O GLU G 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 296 through 297 removed outlier: 6.576A pdb=" N ARG G 296 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 317 through 318 Processing sheet with id=AE3, first strand: chain 'H' and resid 272 through 274 Processing sheet with id=AE4, first strand: chain 'H' and resid 296 through 297 removed outlier: 6.522A pdb=" N ARG H 296 " --> pdb=" O LEU H 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 317 through 318 removed outlier: 5.940A pdb=" N ALA I 14 " --> pdb=" O ILE I 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 272 through 274 Processing sheet with id=AE7, first strand: chain 'I' and resid 296 through 297 removed outlier: 6.542A pdb=" N ARG I 296 " --> pdb=" O LEU I 308 " (cutoff:3.500A) 1488 hydrogen bonds defined for protein. 4260 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: 6.58 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7701 1.33 - 1.45: 4434 1.45 - 1.57: 16308 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 28611 Sorted by residual: bond pdb=" N VAL F 295 " pdb=" CA VAL F 295 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.11e-02 8.12e+03 1.00e+01 bond pdb=" N VAL E 295 " pdb=" CA VAL E 295 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.48e+00 bond pdb=" N VAL I 283 " pdb=" CA VAL I 283 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.45e+00 bond pdb=" N VAL D 295 " pdb=" CA VAL D 295 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.24e-02 6.50e+03 7.84e+00 bond pdb=" N LYS I 312 " pdb=" CA LYS I 312 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.67e+00 ... (remaining 28606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 37984 1.55 - 3.09: 764 3.09 - 4.64: 96 4.64 - 6.19: 37 6.19 - 7.73: 5 Bond angle restraints: 38886 Sorted by residual: angle pdb=" CA ALA E 294 " pdb=" C ALA E 294 " pdb=" O ALA E 294 " ideal model delta sigma weight residual 121.56 117.79 3.77 1.09e+00 8.42e-01 1.20e+01 angle pdb=" CA ALA I 294 " pdb=" C ALA I 294 " pdb=" O ALA I 294 " ideal model delta sigma weight residual 122.41 118.44 3.97 1.21e+00 6.83e-01 1.08e+01 angle pdb=" CB GLN F 293 " pdb=" CG GLN F 293 " pdb=" CD GLN F 293 " ideal model delta sigma weight residual 112.60 107.12 5.48 1.70e+00 3.46e-01 1.04e+01 angle pdb=" CA SER I 288 " pdb=" C SER I 288 " pdb=" O SER I 288 " ideal model delta sigma weight residual 121.84 118.22 3.62 1.16e+00 7.43e-01 9.74e+00 angle pdb=" CA VAL F 295 " pdb=" C VAL F 295 " pdb=" O VAL F 295 " ideal model delta sigma weight residual 121.63 118.59 3.04 9.90e-01 1.02e+00 9.40e+00 ... (remaining 38881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15851 17.95 - 35.91: 1111 35.91 - 53.86: 195 53.86 - 71.81: 36 71.81 - 89.77: 33 Dihedral angle restraints: 17226 sinusoidal: 6858 harmonic: 10368 Sorted by residual: dihedral pdb=" CA TYR A 820 " pdb=" C TYR A 820 " pdb=" N ASP A 821 " pdb=" CA ASP A 821 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TYR B 820 " pdb=" C TYR B 820 " pdb=" N ASP B 821 " pdb=" CA ASP B 821 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LEU C 210 " pdb=" C LEU C 210 " pdb=" N GLU C 211 " pdb=" CA GLU C 211 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 17223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3311 0.042 - 0.083: 854 0.083 - 0.125: 329 0.125 - 0.167: 21 0.167 - 0.208: 6 Chirality restraints: 4521 Sorted by residual: chirality pdb=" CA LEU A 717 " pdb=" N LEU A 717 " pdb=" C LEU A 717 " pdb=" CB LEU A 717 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG I 292 " pdb=" N ARG I 292 " pdb=" C ARG I 292 " pdb=" CB ARG I 292 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA VAL F 295 " pdb=" N VAL F 295 " pdb=" C VAL F 295 " pdb=" CB VAL F 295 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 4518 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 434 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO A 435 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 434 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO C 435 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 435 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 435 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 126 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLN C 126 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN C 126 " 0.011 2.00e-02 2.50e+03 pdb=" N SER C 127 " 0.010 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1970 2.74 - 3.28: 27371 3.28 - 3.82: 44149 3.82 - 4.36: 51274 4.36 - 4.90: 92556 Nonbonded interactions: 217320 Sorted by model distance: nonbonded pdb=" CH2 TRP I 281 " pdb=" CG GLU I 327 " model vdw 2.198 3.740 nonbonded pdb=" OG SER C 718 " pdb=" OG1 THR C 794 " model vdw 2.200 3.040 nonbonded pdb=" NH2 ARG B 421 " pdb=" O LEU B 491 " model vdw 2.219 3.120 nonbonded pdb=" NH2 ARG A 421 " pdb=" O LEU A 491 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASP B 78 " pdb=" NZ LYS C 290 " model vdw 2.226 3.120 ... (remaining 217315 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 12 through 19 or resid 266 through 343)) selection = (chain 'E' and (resid 12 through 19 or resid 266 through 343)) selection = (chain 'F' and (resid 12 through 19 or resid 266 through 343)) selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.500 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28611 Z= 0.175 Angle : 0.543 7.734 38886 Z= 0.293 Chirality : 0.042 0.208 4521 Planarity : 0.004 0.044 4992 Dihedral : 13.230 89.766 10530 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.71 % Allowed : 0.40 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3576 helix: 1.45 (0.13), residues: 1584 sheet: -0.03 (0.22), residues: 534 loop : -0.83 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 809 TYR 0.013 0.001 TYR B 797 PHE 0.021 0.001 PHE A 749 TRP 0.011 0.001 TRP C 526 HIS 0.004 0.001 HIS C 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (28611) covalent geometry : angle 0.54309 / 0.29 (38886) hydrogen bonds : bond 0.21229 / 13.88 ( 1488) hydrogen bonds : angle 6.69299 / 4.87 ( 4260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 460 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8786 (tt) cc_final: 0.8574 (tp) REVERT: A 208 LYS cc_start: 0.9227 (tmmt) cc_final: 0.9000 (tppp) REVERT: B 218 SER cc_start: 0.7638 (m) cc_final: 0.7406 (m) REVERT: B 723 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7434 (mtp85) REVERT: B 911 PHE cc_start: 0.8781 (m-80) cc_final: 0.8415 (m-80) REVERT: C 13 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7907 (mtp180) REVERT: C 278 MET cc_start: 0.9212 (mmt) cc_final: 0.8619 (mmt) REVERT: C 330 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8063 (ttp-110) REVERT: C 519 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7821 (mtm-85) REVERT: C 769 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7561 (mtt90) REVERT: C 977 MET cc_start: 0.8498 (mmt) cc_final: 0.8295 (mmt) REVERT: D 289 THR cc_start: 0.8365 (m) cc_final: 0.8124 (p) REVERT: D 292 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8410 (ttp-110) REVERT: D 326 ARG cc_start: 0.7956 (ptt90) cc_final: 0.7685 (ptt90) REVERT: E 20 GLN cc_start: 0.8509 (pp30) cc_final: 0.8118 (pp30) REVERT: F 18 GLN cc_start: 0.9176 (mt0) cc_final: 0.8281 (mt0) REVERT: I 288 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6112 (p) REVERT: I 293 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7013 (tp-100) REVERT: I 315 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7588 (m-30) outliers start: 21 outliers final: 14 residues processed: 481 average time/residue: 0.8280 time to fit residues: 451.4108 Evaluate side-chains 283 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 291 ARG Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 326 ARG Chi-restraints excluded: chain I residue 327 GLU Chi-restraints excluded: chain I residue 329 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 129 GLN A 167 GLN A 311 GLN A 325 GLN A 500 GLN B 167 GLN B 325 GLN B 454 GLN C 167 GLN C 379 HIS E 18 GLN I 329 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081171 restraints weight = 45680.889| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.84 r_work: 0.2901 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28611 Z= 0.151 Angle : 0.575 10.155 38886 Z= 0.294 Chirality : 0.043 0.207 4521 Planarity : 0.005 0.046 4992 Dihedral : 6.314 86.616 3991 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.06 % Allowed : 10.11 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3576 helix: 1.94 (0.13), residues: 1626 sheet: -0.10 (0.22), residues: 576 loop : -0.78 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 338 TYR 0.012 0.001 TYR B 797 PHE 0.015 0.001 PHE B 85 TRP 0.019 0.001 TRP I 316 HIS 0.004 0.001 HIS B 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (28611) covalent geometry : angle 0.57503 / 0.29 (38886) hydrogen bonds : bond 0.05800 / 3.80 ( 1488) hydrogen bonds : angle 4.80773 / 3.52 ( 4260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8356 (m-30) cc_final: 0.8100 (m-30) REVERT: A 199 LEU cc_start: 0.9003 (mp) cc_final: 0.8709 (tp) REVERT: A 208 LYS cc_start: 0.9227 (tmmt) cc_final: 0.9015 (tmmt) REVERT: A 634 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 249 ARG cc_start: 0.8163 (ptm-80) cc_final: 0.7827 (ppp80) REVERT: B 300 LYS cc_start: 0.8965 (mtpm) cc_final: 0.8643 (mttp) REVERT: B 911 PHE cc_start: 0.8526 (m-80) cc_final: 0.8174 (m-80) REVERT: C 13 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.8102 (mtp180) REVERT: C 96 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7913 (mpp) REVERT: C 330 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7764 (ttp-110) REVERT: C 342 GLU cc_start: 0.8550 (tt0) cc_final: 0.8267 (mt-10) REVERT: C 519 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7750 (mtm-85) REVERT: C 723 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7870 (mtp85) REVERT: E 20 GLN cc_start: 0.8511 (pp30) cc_final: 0.8128 (pp30) REVERT: E 330 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8993 (tt0) REVERT: F 18 GLN cc_start: 0.8754 (mt0) cc_final: 0.8474 (mt0) REVERT: F 304 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7535 (mmm160) REVERT: I 309 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8194 (pm20) outliers start: 61 outliers final: 28 residues processed: 337 average time/residue: 0.7881 time to fit residues: 303.1541 Evaluate side-chains 299 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 291 ARG Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 327 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 333 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 327 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 346 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 325 GLN C 167 GLN C 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076448 restraints weight = 46864.352| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.77 r_work: 0.2882 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28611 Z= 0.146 Angle : 0.539 7.001 38886 Z= 0.274 Chirality : 0.042 0.176 4521 Planarity : 0.004 0.046 4992 Dihedral : 5.808 89.406 3972 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 2.73 % Allowed : 11.83 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3576 helix: 2.00 (0.13), residues: 1635 sheet: 0.04 (0.22), residues: 543 loop : -0.77 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 253 TYR 0.012 0.001 TYR B 797 PHE 0.016 0.001 PHE B 85 TRP 0.013 0.001 TRP C 952 HIS 0.003 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (28611) covalent geometry : angle 0.53933 / 0.27 (38886) hydrogen bonds : bond 0.05007 / 3.30 ( 1488) hydrogen bonds : angle 4.46057 / 3.26 ( 4260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8378 (m-30) cc_final: 0.7911 (m-30) REVERT: A 199 LEU cc_start: 0.9093 (mp) cc_final: 0.8784 (tp) REVERT: A 208 LYS cc_start: 0.9213 (tmmt) cc_final: 0.9003 (tmmt) REVERT: A 311 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8581 (pp30) REVERT: A 634 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 749 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7593 (t80) REVERT: B 29 LEU cc_start: 0.8440 (mp) cc_final: 0.8040 (tt) REVERT: B 159 ASP cc_start: 0.8691 (t0) cc_final: 0.8297 (m-30) REVERT: B 550 ARG cc_start: 0.7512 (mmt-90) cc_final: 0.7224 (mpp-170) REVERT: B 911 PHE cc_start: 0.8604 (m-80) cc_final: 0.8165 (m-80) REVERT: C 13 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.8001 (mtp180) REVERT: C 96 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.7834 (mpp) REVERT: C 208 LYS cc_start: 0.9159 (tmmm) cc_final: 0.8901 (tmmt) REVERT: C 330 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7748 (ttp-110) REVERT: C 342 GLU cc_start: 0.8569 (tt0) cc_final: 0.8261 (mt-10) REVERT: C 723 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: E 20 GLN cc_start: 0.8616 (pp30) cc_final: 0.8052 (pp30) REVERT: E 302 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7934 (mp0) REVERT: E 304 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7260 (mtp85) REVERT: F 18 GLN cc_start: 0.8901 (mt0) cc_final: 0.8501 (mt0) REVERT: F 296 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8050 (ttm170) REVERT: F 309 GLU cc_start: 0.8447 (pp20) cc_final: 0.8245 (pt0) outliers start: 81 outliers final: 34 residues processed: 340 average time/residue: 0.7394 time to fit residues: 289.0229 Evaluate side-chains 302 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 500 GLN A 518 GLN C 92 GLN C 325 GLN C 862 GLN D 277 GLN F 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.077695 restraints weight = 46491.406| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.76 r_work: 0.2875 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28611 Z= 0.139 Angle : 0.535 9.191 38886 Z= 0.269 Chirality : 0.042 0.173 4521 Planarity : 0.004 0.045 4992 Dihedral : 5.409 89.592 3954 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 3.10 % Allowed : 12.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3576 helix: 2.09 (0.13), residues: 1635 sheet: 0.11 (0.22), residues: 540 loop : -0.73 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 249 TYR 0.010 0.001 TYR B 797 PHE 0.016 0.001 PHE B 85 TRP 0.012 0.001 TRP C 952 HIS 0.003 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (28611) covalent geometry : angle 0.53457 / 0.27 (38886) hydrogen bonds : bond 0.04614 / 3.05 ( 1488) hydrogen bonds : angle 4.30481 / 3.15 ( 4260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8365 (m-30) cc_final: 0.7892 (m-30) REVERT: A 199 LEU cc_start: 0.9136 (mp) cc_final: 0.8843 (tp) REVERT: A 208 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8992 (tmmt) REVERT: A 311 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (pp30) REVERT: A 450 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 634 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 1019 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: B 29 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 159 ASP cc_start: 0.8675 (t0) cc_final: 0.8274 (m-30) REVERT: B 550 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7196 (mpp-170) REVERT: B 911 PHE cc_start: 0.8574 (m-80) cc_final: 0.8142 (m-80) REVERT: C 96 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: C 110 TRP cc_start: 0.9456 (OUTLIER) cc_final: 0.8791 (m100) REVERT: C 126 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8200 (mp-120) REVERT: C 208 LYS cc_start: 0.9132 (tmmm) cc_final: 0.8924 (ttpp) REVERT: C 330 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7727 (ttp-110) REVERT: C 497 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 723 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: E 20 GLN cc_start: 0.8669 (pp30) cc_final: 0.8120 (pp30) REVERT: E 304 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7308 (mtp85) REVERT: E 312 LYS cc_start: 0.9238 (mmtp) cc_final: 0.9017 (mppt) REVERT: E 330 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8994 (tt0) REVERT: F 18 GLN cc_start: 0.8919 (mt0) cc_final: 0.8541 (mt0) REVERT: F 304 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7114 (mmm160) outliers start: 92 outliers final: 44 residues processed: 346 average time/residue: 0.7171 time to fit residues: 285.8007 Evaluate side-chains 319 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 239 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 100 optimal weight: 0.0770 chunk 311 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 156 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.338 > 50:) chunk 198 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 500 GLN C 325 GLN C 739 GLN C 862 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080159 restraints weight = 46223.758| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.75 r_work: 0.2916 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28611 Z= 0.102 Angle : 0.505 8.426 38886 Z= 0.253 Chirality : 0.040 0.159 4521 Planarity : 0.004 0.044 4992 Dihedral : 5.286 89.042 3954 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 2.63 % Allowed : 13.72 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3576 helix: 2.24 (0.13), residues: 1635 sheet: 0.16 (0.22), residues: 570 loop : -0.70 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 769 TYR 0.010 0.001 TYR B 154 PHE 0.014 0.001 PHE C 516 TRP 0.012 0.001 TRP B 952 HIS 0.002 0.000 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (28611) covalent geometry : angle 0.50515 / 0.25 (38886) hydrogen bonds : bond 0.03909 / 2.59 ( 1488) hydrogen bonds : angle 4.14713 / 3.03 ( 4260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8143 (m-30) cc_final: 0.7600 (m-30) REVERT: A 199 LEU cc_start: 0.9145 (mp) cc_final: 0.8828 (tp) REVERT: A 208 LYS cc_start: 0.9202 (tmmt) cc_final: 0.8973 (tmmt) REVERT: A 311 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: A 450 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 634 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 749 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7514 (t80) REVERT: B 11 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7604 (mt0) REVERT: B 29 LEU cc_start: 0.8452 (mp) cc_final: 0.8069 (tt) REVERT: B 126 GLN cc_start: 0.8489 (pm20) cc_final: 0.8172 (mp10) REVERT: B 159 ASP cc_start: 0.8496 (t0) cc_final: 0.8183 (m-30) REVERT: B 189 ILE cc_start: 0.8967 (tt) cc_final: 0.8623 (mt) REVERT: B 550 ARG cc_start: 0.7510 (mmt-90) cc_final: 0.7210 (mpp-170) REVERT: B 723 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7515 (mtp-110) REVERT: B 736 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8619 (tp-100) REVERT: B 911 PHE cc_start: 0.8647 (m-80) cc_final: 0.8221 (m-80) REVERT: C 208 LYS cc_start: 0.9093 (tmmm) cc_final: 0.8889 (ttpp) REVERT: C 330 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7610 (ttp-110) REVERT: C 723 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7851 (mtp85) REVERT: C 1017 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: E 20 GLN cc_start: 0.8616 (pp30) cc_final: 0.8016 (pp30) REVERT: E 304 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7251 (mtp85) REVERT: E 330 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8943 (tt0) REVERT: F 18 GLN cc_start: 0.8887 (mt0) cc_final: 0.8503 (mt0) REVERT: F 277 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8385 (tm-30) REVERT: F 296 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8356 (ttp80) REVERT: F 304 ARG cc_start: 0.7573 (mtp85) cc_final: 0.7037 (mmm160) REVERT: F 309 GLU cc_start: 0.8526 (pt0) cc_final: 0.7835 (pt0) outliers start: 78 outliers final: 30 residues processed: 358 average time/residue: 0.7135 time to fit residues: 296.2862 Evaluate side-chains 316 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 0.0050 chunk 278 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 222 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 500 GLN C 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.079905 restraints weight = 46257.243| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.76 r_work: 0.2931 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28611 Z= 0.100 Angle : 0.505 9.364 38886 Z= 0.250 Chirality : 0.040 0.134 4521 Planarity : 0.004 0.042 4992 Dihedral : 5.084 89.497 3952 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 2.39 % Allowed : 15.00 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 3576 helix: 2.31 (0.13), residues: 1635 sheet: 0.21 (0.22), residues: 570 loop : -0.65 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 496 TYR 0.010 0.001 TYR C 154 PHE 0.013 0.001 PHE B 95 TRP 0.011 0.001 TRP C 952 HIS 0.002 0.000 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (28611) covalent geometry : angle 0.50486 / 0.25 (38886) hydrogen bonds : bond 0.03665 / 2.43 ( 1488) hydrogen bonds : angle 4.03678 / 2.94 ( 4260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 298 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8350 (m-30) cc_final: 0.7827 (m-30) REVERT: A 199 LEU cc_start: 0.9194 (mp) cc_final: 0.8837 (tp) REVERT: A 208 LYS cc_start: 0.9206 (tmmt) cc_final: 0.8834 (tmmt) REVERT: A 311 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8520 (pp30) REVERT: A 450 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 634 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 749 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 29 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8115 (tt) REVERT: B 96 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8828 (mpt) REVERT: B 159 ASP cc_start: 0.8634 (t0) cc_final: 0.8293 (m-30) REVERT: B 189 ILE cc_start: 0.9065 (tt) cc_final: 0.8697 (mt) REVERT: B 550 ARG cc_start: 0.7461 (mmt-90) cc_final: 0.7136 (mpp-170) REVERT: B 736 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8682 (tp-100) REVERT: B 911 PHE cc_start: 0.8572 (m-80) cc_final: 0.8145 (m-80) REVERT: B 944 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: C 208 LYS cc_start: 0.9079 (tmmm) cc_final: 0.8853 (ttpp) REVERT: C 330 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7659 (ttp-110) REVERT: C 551 LEU cc_start: 0.8413 (tt) cc_final: 0.8133 (tt) REVERT: C 723 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: C 1017 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.7936 (mtm-85) REVERT: E 20 GLN cc_start: 0.8662 (pp30) cc_final: 0.8052 (pp30) REVERT: E 304 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7316 (mtp85) REVERT: F 18 GLN cc_start: 0.8856 (mt0) cc_final: 0.8433 (mt0) REVERT: F 20 GLN cc_start: 0.8271 (mp10) cc_final: 0.8020 (mm-40) REVERT: F 277 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8385 (tm-30) REVERT: F 284 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8082 (mt-10) REVERT: F 296 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8346 (ttp80) REVERT: F 309 GLU cc_start: 0.8570 (pt0) cc_final: 0.7853 (pt0) outliers start: 71 outliers final: 38 residues processed: 347 average time/residue: 0.7182 time to fit residues: 288.9775 Evaluate side-chains 322 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 947 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 68 optimal weight: 0.0270 chunk 248 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 345 optimal weight: 0.0570 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 417 GLN A 500 GLN C 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080170 restraints weight = 46202.315| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.76 r_work: 0.2938 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28611 Z= 0.100 Angle : 0.509 10.220 38886 Z= 0.251 Chirality : 0.040 0.139 4521 Planarity : 0.004 0.052 4992 Dihedral : 4.935 89.951 3950 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 2.39 % Allowed : 15.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3576 helix: 2.36 (0.13), residues: 1635 sheet: 0.24 (0.22), residues: 570 loop : -0.63 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 785 TYR 0.010 0.001 TYR C 154 PHE 0.021 0.001 PHE C 516 TRP 0.010 0.001 TRP B 952 HIS 0.002 0.000 HIS B 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (28611) covalent geometry : angle 0.50927 / 0.25 (38886) hydrogen bonds : bond 0.03529 / 2.35 ( 1488) hydrogen bonds : angle 3.96803 / 2.89 ( 4260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8132 (m-30) cc_final: 0.7575 (m-30) REVERT: A 199 LEU cc_start: 0.9151 (mp) cc_final: 0.8795 (tp) REVERT: A 208 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8772 (tmmt) REVERT: A 311 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: A 450 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (mp) REVERT: A 634 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 749 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7567 (t80) REVERT: A 909 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7178 (mt) REVERT: B 29 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 96 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8612 (mpt) REVERT: B 126 GLN cc_start: 0.8465 (pm20) cc_final: 0.8213 (mp10) REVERT: B 159 ASP cc_start: 0.8457 (t0) cc_final: 0.8149 (m-30) REVERT: B 189 ILE cc_start: 0.8991 (tt) cc_final: 0.8625 (mt) REVERT: B 454 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8556 (mm-40) REVERT: B 550 ARG cc_start: 0.7472 (mmt-90) cc_final: 0.7176 (mpp-170) REVERT: B 736 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8597 (tp-100) REVERT: B 911 PHE cc_start: 0.8607 (m-80) cc_final: 0.8224 (m-80) REVERT: B 944 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: C 208 LYS cc_start: 0.9092 (tmmm) cc_final: 0.8878 (ttpp) REVERT: C 330 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7620 (ttp-110) REVERT: C 551 LEU cc_start: 0.8436 (tt) cc_final: 0.8171 (tt) REVERT: C 723 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7865 (mtp85) REVERT: C 1017 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7824 (mtm-85) REVERT: E 20 GLN cc_start: 0.8651 (pp30) cc_final: 0.8044 (pp30) REVERT: E 304 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7199 (mtp85) REVERT: F 18 GLN cc_start: 0.8854 (mt0) cc_final: 0.8366 (mt0) REVERT: F 20 GLN cc_start: 0.8308 (mp10) cc_final: 0.8026 (mm-40) REVERT: F 277 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8470 (tm-30) REVERT: F 284 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8055 (mt-10) REVERT: F 296 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8279 (ttp80) REVERT: F 309 GLU cc_start: 0.8495 (pt0) cc_final: 0.7574 (pt0) outliers start: 71 outliers final: 41 residues processed: 333 average time/residue: 0.7154 time to fit residues: 276.8281 Evaluate side-chains 329 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 947 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 3.9990 chunk 309 optimal weight: 0.0470 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 345 optimal weight: 40.0000 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.078158 restraints weight = 46592.565| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.77 r_work: 0.2894 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28611 Z= 0.150 Angle : 0.544 9.800 38886 Z= 0.271 Chirality : 0.042 0.176 4521 Planarity : 0.004 0.058 4992 Dihedral : 5.054 89.022 3950 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 2.49 % Allowed : 15.40 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 3576 helix: 2.32 (0.13), residues: 1638 sheet: 0.25 (0.23), residues: 540 loop : -0.61 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 496 TYR 0.046 0.001 TYR B 820 PHE 0.018 0.001 PHE B 85 TRP 0.011 0.001 TRP B 708 HIS 0.003 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (28611) covalent geometry : angle 0.54428 / 0.27 (38886) hydrogen bonds : bond 0.04258 / 2.83 ( 1488) hydrogen bonds : angle 4.04235 / 2.95 ( 4260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8449 (m-30) cc_final: 0.7934 (m-30) REVERT: A 199 LEU cc_start: 0.9228 (mp) cc_final: 0.8869 (tp) REVERT: A 208 LYS cc_start: 0.9081 (tmmt) cc_final: 0.8794 (tmmt) REVERT: A 311 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8574 (pp30) REVERT: A 335 GLU cc_start: 0.8415 (pp20) cc_final: 0.8131 (pp20) REVERT: A 450 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 633 ASP cc_start: 0.8291 (p0) cc_final: 0.7841 (p0) REVERT: A 634 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8502 (mt) REVERT: A 635 GLU cc_start: 0.8346 (mp0) cc_final: 0.8133 (mp0) REVERT: B 29 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8087 (tt) REVERT: B 96 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (mpt) REVERT: B 126 GLN cc_start: 0.8610 (pm20) cc_final: 0.8275 (mp-120) REVERT: B 159 ASP cc_start: 0.8635 (t0) cc_final: 0.8266 (m-30) REVERT: B 162 ASP cc_start: 0.8697 (m-30) cc_final: 0.8490 (m-30) REVERT: B 550 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7199 (mpp-170) REVERT: B 736 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8722 (tp-100) REVERT: B 911 PHE cc_start: 0.8591 (m-80) cc_final: 0.8204 (m-80) REVERT: B 944 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: C 96 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.7858 (mpp) REVERT: C 199 LEU cc_start: 0.9169 (mp) cc_final: 0.8629 (tp) REVERT: C 208 LYS cc_start: 0.9093 (tmmm) cc_final: 0.8888 (ttpp) REVERT: C 330 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7724 (ttp-110) REVERT: C 344 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 723 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8017 (mtp85) REVERT: C 1017 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: E 20 GLN cc_start: 0.8716 (pp30) cc_final: 0.8234 (pp30) REVERT: F 18 GLN cc_start: 0.8865 (mt0) cc_final: 0.8425 (mt0) REVERT: F 20 GLN cc_start: 0.8325 (mp10) cc_final: 0.8066 (mm-40) REVERT: F 277 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8422 (tm-30) REVERT: F 284 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8003 (mt-10) REVERT: F 296 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8288 (ttp80) REVERT: F 309 GLU cc_start: 0.8572 (pt0) cc_final: 0.7684 (pt0) outliers start: 74 outliers final: 40 residues processed: 325 average time/residue: 0.7325 time to fit residues: 275.8279 Evaluate side-chains 327 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 527 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 920 MET Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 270 optimal weight: 0.9990 chunk 180 optimal weight: 0.3980 chunk 284 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 268 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 198 optimal weight: 0.0170 chunk 352 optimal weight: 0.9980 chunk 338 optimal weight: 20.0000 chunk 319 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN C 325 GLN E 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081169 restraints weight = 46436.980| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.73 r_work: 0.2934 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28611 Z= 0.098 Angle : 0.513 9.236 38886 Z= 0.253 Chirality : 0.040 0.139 4521 Planarity : 0.004 0.058 4992 Dihedral : 4.973 89.902 3950 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 1.82 % Allowed : 16.11 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3576 helix: 2.41 (0.13), residues: 1635 sheet: 0.28 (0.22), residues: 570 loop : -0.61 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 496 TYR 0.010 0.001 TYR C 154 PHE 0.011 0.001 PHE B 95 TRP 0.014 0.001 TRP B 952 HIS 0.002 0.000 HIS B 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (28611) covalent geometry : angle 0.51292 / 0.25 (38886) hydrogen bonds : bond 0.03442 / 2.29 ( 1488) hydrogen bonds : angle 3.93703 / 2.87 ( 4260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 295 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 162 ASP cc_start: 0.8141 (m-30) cc_final: 0.7562 (m-30) REVERT: A 199 LEU cc_start: 0.9139 (mp) cc_final: 0.8772 (tp) REVERT: A 208 LYS cc_start: 0.9073 (tmmt) cc_final: 0.8786 (tmmt) REVERT: A 311 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8432 (pp30) REVERT: A 450 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 633 ASP cc_start: 0.8079 (p0) cc_final: 0.7651 (p0) REVERT: A 634 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 29 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 96 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8611 (mpt) REVERT: B 126 GLN cc_start: 0.8464 (pm20) cc_final: 0.8203 (mp10) REVERT: B 159 ASP cc_start: 0.8454 (t0) cc_final: 0.8147 (m-30) REVERT: B 550 ARG cc_start: 0.7489 (mmt-90) cc_final: 0.7192 (mpp-170) REVERT: B 736 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8603 (tp-100) REVERT: B 769 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8574 (mtm180) REVERT: B 911 PHE cc_start: 0.8594 (m-80) cc_final: 0.8225 (m-80) REVERT: B 944 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: C 96 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7609 (mpp) REVERT: C 199 LEU cc_start: 0.9141 (mp) cc_final: 0.8609 (tp) REVERT: C 208 LYS cc_start: 0.9029 (tmmm) cc_final: 0.8771 (tmmt) REVERT: C 330 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7622 (ttp-110) REVERT: C 723 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: C 1017 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: E 20 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (pp30) REVERT: F 18 GLN cc_start: 0.8843 (mt0) cc_final: 0.8337 (mt0) REVERT: F 20 GLN cc_start: 0.8316 (mp10) cc_final: 0.8020 (mm-40) REVERT: F 277 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8412 (tm-30) REVERT: F 296 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8277 (ttp80) REVERT: F 309 GLU cc_start: 0.8460 (pt0) cc_final: 0.7564 (pt0) outliers start: 54 outliers final: 26 residues processed: 328 average time/residue: 0.6831 time to fit residues: 260.0028 Evaluate side-chains 317 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 947 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 70 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 344 optimal weight: 30.0000 chunk 282 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 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 = 0.3629 r_free = 0.3629 target = 0.117070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.076593 restraints weight = 46404.537| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.76 r_work: 0.2872 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28611 Z= 0.171 Angle : 0.563 9.111 38886 Z= 0.281 Chirality : 0.042 0.166 4521 Planarity : 0.004 0.069 4992 Dihedral : 5.106 89.779 3950 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 1.62 % Allowed : 16.48 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.15), residues: 3576 helix: 2.33 (0.13), residues: 1638 sheet: 0.28 (0.23), residues: 540 loop : -0.58 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 496 TYR 0.011 0.001 TYR C 154 PHE 0.026 0.001 PHE C 516 TRP 0.014 0.001 TRP B 708 HIS 0.003 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (28611) covalent geometry : angle 0.56304 / 0.28 (38886) hydrogen bonds : bond 0.04488 / 2.98 ( 1488) hydrogen bonds : angle 4.05749 / 2.96 ( 4260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8611 (p0) REVERT: A 162 ASP cc_start: 0.8466 (m-30) cc_final: 0.7946 (m-30) REVERT: A 199 LEU cc_start: 0.9269 (mp) cc_final: 0.8911 (tp) REVERT: A 208 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8818 (tmmt) REVERT: A 311 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8541 (pp30) REVERT: A 335 GLU cc_start: 0.8431 (pp20) cc_final: 0.8152 (pp20) REVERT: A 450 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 633 ASP cc_start: 0.8285 (p0) cc_final: 0.7839 (p0) REVERT: A 634 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 29 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 96 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8838 (mpt) REVERT: B 126 GLN cc_start: 0.8607 (pm20) cc_final: 0.8253 (mp10) REVERT: B 159 ASP cc_start: 0.8647 (t0) cc_final: 0.8259 (m-30) REVERT: B 162 ASP cc_start: 0.8733 (m-30) cc_final: 0.8507 (m-30) REVERT: B 550 ARG cc_start: 0.7494 (mmt-90) cc_final: 0.7177 (mpp-170) REVERT: B 736 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8728 (tp-100) REVERT: B 769 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8614 (mtm180) REVERT: B 911 PHE cc_start: 0.8554 (m-80) cc_final: 0.8167 (m-80) REVERT: B 944 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: C 96 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.7818 (mpp) REVERT: C 110 TRP cc_start: 0.9451 (OUTLIER) cc_final: 0.8894 (m100) REVERT: C 199 LEU cc_start: 0.9201 (mp) cc_final: 0.8666 (tp) REVERT: C 330 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7728 (ttp-110) REVERT: C 723 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8033 (mtp85) REVERT: C 977 MET cc_start: 0.7532 (mmt) cc_final: 0.7331 (mmt) REVERT: C 1017 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: E 20 GLN cc_start: 0.8874 (pp30) cc_final: 0.8536 (pp30) REVERT: F 20 GLN cc_start: 0.8308 (mp10) cc_final: 0.8063 (mm-40) REVERT: F 277 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8388 (tm-30) REVERT: F 296 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8260 (ttp80) REVERT: F 309 GLU cc_start: 0.8525 (pt0) cc_final: 0.7621 (pt0) outliers start: 48 outliers final: 34 residues processed: 313 average time/residue: 0.6930 time to fit residues: 250.8945 Evaluate side-chains 320 residues out of total 2967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 167 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 348 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN C 325 GLN E 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076792 restraints weight = 46410.022| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.76 r_work: 0.2884 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28611 Z= 0.126 Angle : 0.536 9.487 38886 Z= 0.266 Chirality : 0.041 0.151 4521 Planarity : 0.004 0.063 4992 Dihedral : 5.102 89.848 3950 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 1.69 % Allowed : 16.58 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3576 helix: 2.36 (0.13), residues: 1635 sheet: 0.28 (0.23), residues: 540 loop : -0.58 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 496 TYR 0.010 0.001 TYR C 154 PHE 0.015 0.001 PHE B 85 TRP 0.011 0.001 TRP C 952 HIS 0.003 0.001 HIS B 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (28611) covalent geometry : angle 0.53628 / 0.27 (38886) hydrogen bonds : bond 0.04088 / 2.72 ( 1488) hydrogen bonds : angle 4.03069 / 2.94 ( 4260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13400.24 seconds wall clock time: 227 minutes 44.65 seconds (13664.65 seconds total)