Starting phenix.real_space_refine on Sun Sep 13 09:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5p_12043/09_2026/7b5p_12043.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14522 2.51 5 N 3701 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22527 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7504 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 969} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 6, 'ASP:plan': 7, 'ARG:plan': 7, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 7623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7623 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 969} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 7400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7400 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 942} Chain breaks: 7 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 4.82, per 1000 atoms: 0.21 Number of scatterers: 22527 At special positions: 0 Unit cell: (116.63, 120.91, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4184 8.00 N 3701 7.00 C 14522 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: 2.04 Conformation dependent library (CDL) restraints added in 982.1 milliseconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5532 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 25 sheets defined 53.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'B' and resid 2 through 7 removed outlier: 4.038A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.584A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.626A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.695A pdb=" N ALA B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.914A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 298 through 312 Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.956A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.579A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 4.254A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 removed outlier: 4.019A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.592A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 465 through 486 removed outlier: 4.120A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.862A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 535 removed outlier: 3.631A pdb=" N HIS B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 529 " --> pdb=" O HIS B 525 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 558 removed outlier: 3.554A pdb=" N LEU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 602 removed outlier: 3.820A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 655 removed outlier: 4.055A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.730A pdb=" N ALA B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 789 removed outlier: 3.766A pdb=" N ILE B 786 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 849 removed outlier: 3.610A pdb=" N GLU B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 868 removed outlier: 4.019A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 893 removed outlier: 3.877A pdb=" N ILE B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 904 through 920 removed outlier: 4.199A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 951 Processing helix chain 'B' and resid 960 through 970 Processing helix chain 'B' and resid 972 through 981 removed outlier: 3.549A pdb=" N LEU B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 992 Processing helix chain 'B' and resid 997 through 1017 removed outlier: 4.011A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1032 Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.865A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.566A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.944A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 310 Processing helix chain 'C' and resid 330 through 360 removed outlier: 3.506A pdb=" N LYS C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 369 Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.833A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'C' and resid 406 through 422 removed outlier: 3.625A pdb=" N GLU C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 removed outlier: 3.749A pdb=" N ARG C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 450 removed outlier: 3.952A pdb=" N ALA C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.780A pdb=" N PHE C 458 " --> pdb=" O PRO C 455 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 485 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 513 through 533 removed outlier: 4.172A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 558 removed outlier: 3.727A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 545 " --> pdb=" O TYR C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 602 removed outlier: 3.553A pdb=" N THR C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 643 through 655 removed outlier: 3.666A pdb=" N THR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 698 removed outlier: 4.488A pdb=" N THR C 696 " --> pdb=" O HIS C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 743 through 755 removed outlier: 3.821A pdb=" N THR C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.758A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 848 removed outlier: 3.661A pdb=" N MET C 841 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 872 through 893 removed outlier: 3.682A pdb=" N LEU C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 902 Processing helix chain 'C' and resid 905 through 919 removed outlier: 4.255A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 3.932A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 940 " --> pdb=" O GLY C 936 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 942 " --> pdb=" O SER C 938 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 972 through 984 removed outlier: 3.666A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 997 through 1017 removed outlier: 4.398A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1022 Processing helix chain 'C' and resid 1023 through 1033 removed outlier: 4.304A pdb=" N VAL C1029 " --> pdb=" O PHE C1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.637A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.554A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.557A pdb=" N GLN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.996A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.596A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.636A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.515A pdb=" N LYS A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 342 " --> pdb=" O HIS A 338 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 removed outlier: 3.669A pdb=" N LEU A 366 " --> pdb=" O ARG A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 367 through 387 Proline residue: A 373 - end of helix removed outlier: 3.617A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 402 through 423 removed outlier: 5.105A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.606A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 4.047A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 464 through 497 removed outlier: 4.013A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 540 through 543 removed outlier: 4.038A pdb=" N VAL A 543 " --> pdb=" O ARG A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 543' Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.649A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.063A pdb=" N VAL A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 643 through 654 removed outlier: 4.288A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N THR A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.824A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 860 through 868 removed outlier: 3.541A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.598A pdb=" N LEU A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.981A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 929 through 936 Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.841A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 987 removed outlier: 3.813A pdb=" N THR A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix removed outlier: 3.648A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 990 No H-bonds generated for 'chain 'A' and resid 988 through 990' Processing helix chain 'A' and resid 996 through 1014 removed outlier: 4.216A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1014 " --> pdb=" O GLY A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1033 removed outlier: 3.625A pdb=" N PHE A1021 " --> pdb=" O LEU A1017 " (cutoff:3.500A) Proline residue: A1023 - end of helix removed outlier: 3.726A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1028 " --> pdb=" O VAL A1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 130 removed outlier: 6.814A pdb=" N THR B 87 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN B 89 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 80 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR B 93 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.135A pdb=" N TYR B 327 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 removed outlier: 7.809A pdb=" N TYR B 182 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.440A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.502A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 573 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 713 through 717 removed outlier: 4.227A pdb=" N VAL B 716 " --> pdb=" O LEU B 828 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 828 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 810 through 811 removed outlier: 8.885A pdb=" N ILE A 235 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE B 727 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.756A pdb=" N VAL C 88 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 4.622A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.816A pdb=" N ALA C 286 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 609 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 628 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA C 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 626 " --> pdb=" O ALA C 611 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 613 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR C 624 " --> pdb=" O ASN C 613 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET C 575 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 664 " --> pdb=" O MET C 575 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.817A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 767 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE C 763 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 769 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP C 761 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 771 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 215 through 218 removed outlier: 5.194A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 234 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AB8, first strand: chain 'C' and resid 681 through 682 Processing sheet with id=AB9, first strand: chain 'C' and resid 790 through 792 Processing sheet with id=AC1, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.502A pdb=" N ALA A 47 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 87 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN A 89 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 80 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 93 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.425A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 630 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 322 through 324 removed outlier: 4.425A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 666 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.637A pdb=" N TRP A 187 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.834A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 682 through 685 removed outlier: 3.885A pdb=" N ASP A 858 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 790 through 792 1173 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.64 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: 6763 1.33 - 1.45: 3466 1.45 - 1.57: 12476 1.57 - 1.69: 0 1.69 - 1.82: 234 Bond restraints: 22939 Sorted by residual: bond pdb=" N PRO A 50 " pdb=" CD PRO A 50 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.79e+01 bond pdb=" N PRO A 223 " pdb=" CD PRO A 223 " ideal model delta sigma weight residual 1.474 1.530 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" N THR A 917 " pdb=" CA THR A 917 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.12e-02 7.97e+03 7.27e+00 bond pdb=" N LEU A 913 " pdb=" CA LEU A 913 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 6.92e+00 bond pdb=" N VAL A 909 " pdb=" CA VAL A 909 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.30e-02 5.92e+03 6.87e+00 ... (remaining 22934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 29457 2.00 - 4.01: 1547 4.01 - 6.01: 174 6.01 - 8.01: 25 8.01 - 10.02: 8 Bond angle restraints: 31211 Sorted by residual: angle pdb=" C PHE B 317 " pdb=" N PRO B 318 " pdb=" CA PRO B 318 " ideal model delta sigma weight residual 119.84 128.44 -8.60 1.25e+00 6.40e-01 4.73e+01 angle pdb=" N VAL C 265 " pdb=" CA VAL C 265 " pdb=" C VAL C 265 " ideal model delta sigma weight residual 113.20 106.70 6.50 9.60e-01 1.09e+00 4.58e+01 angle pdb=" C PHE A1021 " pdb=" N VAL A1022 " pdb=" CA VAL A1022 " ideal model delta sigma weight residual 120.43 125.53 -5.10 9.60e-01 1.09e+00 2.83e+01 angle pdb=" C ILE B 367 " pdb=" N PRO B 368 " pdb=" CA PRO B 368 " ideal model delta sigma weight residual 119.64 124.74 -5.10 1.01e+00 9.80e-01 2.55e+01 angle pdb=" C PRO C 426 " pdb=" N PRO C 427 " pdb=" CA PRO C 427 " ideal model delta sigma weight residual 119.84 126.07 -6.23 1.25e+00 6.40e-01 2.49e+01 ... (remaining 31206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12526 18.00 - 35.99: 872 35.99 - 53.99: 192 53.99 - 71.99: 39 71.99 - 89.98: 12 Dihedral angle restraints: 13641 sinusoidal: 5038 harmonic: 8603 Sorted by residual: dihedral pdb=" CA PHE C1025 " pdb=" C PHE C1025 " pdb=" N PHE C1026 " pdb=" CA PHE C1026 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA PRO B 579 " pdb=" C PRO B 579 " pdb=" N ALA B 580 " pdb=" CA ALA B 580 " ideal model delta harmonic sigma weight residual 180.00 153.14 26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA THR A 648 " pdb=" C THR A 648 " pdb=" N MET A 649 " pdb=" CA MET A 649 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 13638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3118 0.075 - 0.150: 590 0.150 - 0.224: 41 0.224 - 0.299: 3 0.299 - 0.374: 3 Chirality restraints: 3755 Sorted by residual: chirality pdb=" CA ILE A 534 " pdb=" N ILE A 534 " pdb=" C ILE A 534 " pdb=" CB ILE A 534 " both_signs ideal model delta sigma weight residual False 2.43 2.06 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA GLU B 269 " pdb=" N GLU B 269 " pdb=" C GLU B 269 " pdb=" CB GLU B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA GLU A 842 " pdb=" N GLU A 842 " pdb=" C GLU A 842 " pdb=" CB GLU A 842 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3752 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 374 " 0.020 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C VAL C 374 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL C 374 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 375 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 3 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C ASN A 3 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN A 3 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE A 4 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 762 " 0.007 2.00e-02 2.50e+03 1.76e-02 5.42e+00 pdb=" CG PHE C 762 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 762 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 762 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 762 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 762 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 762 " -0.005 2.00e-02 2.50e+03 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 117 2.50 - 3.10: 16837 3.10 - 3.70: 32541 3.70 - 4.30: 46720 4.30 - 4.90: 80989 Nonbonded interactions: 177204 Sorted by model distance: nonbonded pdb=" O TYR A 857 " pdb=" OD1 ASP A 858 " model vdw 1.894 3.040 nonbonded pdb=" O ASP C 53 " pdb=" OD1 ASP C 53 " model vdw 2.141 3.040 nonbonded pdb=" O GLU A 845 " pdb=" CD GLU A 845 " model vdw 2.148 3.270 nonbonded pdb=" O GLU A 845 " pdb=" OE1 GLU A 845 " model vdw 2.193 3.040 nonbonded pdb=" O LEU C 75 " pdb=" N TYR C 77 " model vdw 2.194 3.120 ... (remaining 177199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 119 or (resid 120 thro \ ugh 121 and (name N or name CA or name C or name O or name CB )) or resid 122 th \ rough 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) \ or resid 126 through 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 134 or resid 136 through 163 or (resid 164 \ through 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 167 or (resid 168 and (name N or name CA or name C or name O or name \ CB )) or resid 169 through 173 or (resid 174 and (name N or name CA or name C or \ name O or name CB )) or resid 175 through 191 or (resid 192 and (name N or name \ CA or name C or name O or name CB )) or resid 193 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB )) or resid 196 through 207 o \ r (resid 208 through 209 and (name N or name CA or name C or name O or name CB ) \ ) or resid 210 through 212 or (resid 213 and (name N or name CA or name C or nam \ e O or name CB )) or resid 214 through 228 or (resid 229 and (name N or name CA \ or name C or name O or name CB )) or resid 230 through 247 or (resid 248 and (na \ me N or name CA or name C or name O or name CB )) or resid 249 or (resid 250 and \ (name N or name CA or name C or name O or name CB )) or resid 251 through 254 o \ r (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 56 through 262 or (resid 263 and (name N or name CA or name C or name O or name \ CB )) or resid 264 through 268 or (resid 269 and (name N or name CA or name C or \ name O or name CB )) or resid 270 through 279 or (resid 280 and (name N or name \ CA or name C or name O or name CB )) or resid 281 through 291 or (resid 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 300 o \ r (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 02 through 341 or (resid 342 and (name N or name CA or name C or name O or name \ CB )) or resid 343 through 397 or (resid 398 and (name N or name CA or name C or \ name O or name CB )) or resid 399 through 403 or (resid 404 through 405 and (na \ me N or name CA or name C or name O or name CB )) or resid 406 through 421 or (r \ esid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 t \ hrough 446 or (resid 447 and (name N or name CA or name C or name O or name CB ) \ ) or resid 448 through 452 or (resid 453 and (name N or name CA or name C or nam \ e CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or \ resid 454 or (resid 455 and (name N or name CA or name C or name O or name CB o \ r name CG )) or resid 456 through 495 or (resid 496 and (name N or name CA or na \ me C or name O or name CB )) or resid 497 or (resid 498 and (name N or name CA o \ r name C or name O or name CB )) or resid 499 through 565 or (resid 566 and (nam \ e N or name CA or name C or name O or name CB )) or resid 567 through 574 or (re \ sid 575 and (name N or name CA or name C or name O or name CB )) or resid 576 th \ rough 602 or (resid 603 and (name N or name CA or name C or name O or name CB )) \ or resid 604 through 616 or (resid 617 through 618 and (name N or name CA or na \ me C or name O or name CB )) or resid 619 or (resid 620 and (name N or name CA o \ r name C or name O or name CB )) or resid 621 through 635 or (resid 636 and (nam \ e N or name CA or name C or name O or name CB )) or resid 637 through 639 or (re \ sid 640 and (name N or name CA or name C or name O or name CB )) or resid 641 th \ rough 644 or (resid 645 through 646 and (name N or name CA or name C or name O o \ r name CB )) or resid 647 through 658 or (resid 659 and (name N or name CA or na \ me C or name O or name CB )) or resid 660 through 672 or resid 678 through 704 o \ r (resid 705 through 707 and (name N or name CA or name C or name O or name CB ) \ ) or resid 708 through 711 or (resid 712 and (name N or name CA or name C or nam \ e O or name CB )) or resid 713 through 727 or (resid 728 and (name N or name CA \ or name C or name O or name CB )) or resid 729 through 736 or (resid 737 through \ 738 and (name N or name CA or name C or name O or name CB )) or resid 739 throu \ gh 740 or resid 742 through 763 or (resid 764 through 765 and (name N or name CA \ or name C or name O or name CB )) or resid 766 or (resid 767 and (name N or nam \ e CA or name C or name O or name CB )) or resid 768 through 775 or (resid 776 th \ rough 778 and (name N or name CA or name C or name O or name CB )) or resid 779 \ through 783 or (resid 784 through 785 and (name N or name CA or name C or name O \ or name CB )) or resid 786 through 793 or resid 796 or (resid 797 and (name N o \ r name CA or name C or name O or name CB )) or resid 798 through 825 or (resid 8 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 827 through \ 898 or (resid 899 and (name N or name CA or name C or name O or name CB )) or r \ esid 900 through 917 or (resid 918 and (name N or name CA or name C or name O or \ name CB )) or resid 919 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 949 or (resid 950 and (name N o \ r name CA or name C or name O or name CB )) or resid 951 through 954 or (resid 9 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 956 through \ 1007 or (resid 1008 and (name N or name CA or name C or name O or name CB )) or \ resid 1009 through 1031 or (resid 1032 and (name N or name CA or name C or name \ O or name CB )) or resid 1033)) selection = (chain 'B' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 52 or (resid 53 through 54 and (nam \ e N or name CA or name C or name O or name CB )) or resid 55 through 66 or (resi \ d 67 and (name N or name CA or name C or name O or name CB )) or resid 68 throug \ h 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) or \ resid 126 through 300 or (resid 301 and (name N or name CA or name C or name O o \ r name CB )) or resid 302 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 407 or (resid 408 through 409 \ and (name N or name CA or name C or name O or name CB )) or resid 410 through 41 \ 9 or (resid 420 through 422 and (name N or name CA or name C or name O or name C \ B )) or resid 423 through 454 or (resid 455 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 456 through 458 or (resid 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 495 or (res \ id 496 and (name N or name CA or name C or name O or name CB )) or resid 497 or \ (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 499 \ or resid 524 through 535 or (resid 536 and (name N or name CA or name C or name \ O or name CB )) or resid 537 through 539 or (resid 540 through 541 and (name N \ or name CA or name C or name O or name CB )) or resid 542 through 543 or (resid \ 544 through 545 and (name N or name CA or name C or name O or name CB )) or resi \ d 546 through 555 or (resid 556 and (name N or name CA or name C or name O or na \ me CB )) or resid 557 through 558 or (resid 559 and (name N or name CA or name C \ or name O or name CB )) or resid 560 or resid 565 through 639 or (resid 640 and \ (name N or name CA or name C or name O or name CB )) or resid 641 through 672 o \ r resid 678 through 709 or resid 711 or (resid 712 and (name N or name CA or nam \ e C or name O or name CB )) or resid 713 through 727 or (resid 728 and (name N o \ r name CA or name C or name O or name CB )) or resid 729 through 740 or resid 74 \ 2 through 793 or resid 796 through 828 or resid 839 through 849 or resid 851 thr \ ough 866 or (resid 867 and (name N or name CA or name C or name O or name CB )) \ or resid 868 or resid 873 through 875 or (resid 876 through 878 and (name N or n \ ame CA or name C or name O or name CB )) or resid 879 through 898 or (resid 899 \ and (name N or name CA or name C or name O or name CB )) or resid 900 through 93 \ 9 or (resid 940 and (name N or name CA or name C or name O or name CB )) or resi \ d 941 through 954 or (resid 955 and (name N or name CA or name C or name O or na \ me CB )) or resid 956 through 1007 or (resid 1008 and (name N or name CA or name \ C or name O or name CB )) or resid 1009 through 1033)) selection = (chain 'C' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 52 or (resid 53 through 54 and (nam \ e N or name CA or name C or name O or name CB )) or resid 55 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 119 or (resid 120 through 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 through 129 or (resid 130 and (name N or name CA or name C \ or name O or name CB )) or resid 131 through 134 or resid 136 through 163 or (r \ esid 164 through 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 167 or (resid 168 and (name N or name CA or name C or name O \ or name CB )) or resid 169 through 173 or (resid 174 and (name N or name CA or n \ ame C or name O or name CB )) or resid 175 through 191 or (resid 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 194 or (resid \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 207 or (resid 208 through 209 and (name N or name CA or name C or name O or n \ ame CB )) or resid 210 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 225 or (resid 226 and (name N or \ name CA or name C or name O or name CB )) or resid 227 through 228 or (resid 229 \ and (name N or name CA or name C or name O or name CB )) or resid 230 through 2 \ 43 or (resid 244 and (name N or name CA or name C or name O or name CB )) or res \ id 245 through 247 or (resid 248 and (name N or name CA or name C or name O or n \ ame CB )) or resid 249 or (resid 250 and (name N or name CA or name C or name O \ or name CB )) or resid 251 through 262 or (resid 263 and (name N or name CA or n \ ame C or name O or name CB )) or resid 264 through 268 or (resid 269 and (name N \ or name CA or name C or name O or name CB )) or resid 270 through 279 or (resid \ 280 and (name N or name CA or name C or name O or name CB )) or resid 281 throu \ gh 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or \ resid 293 through 345 or (resid 346 through 347 and (name N or name CA or name \ C or name O or name CB )) or resid 348 through 403 or (resid 404 through 405 and \ (name N or name CA or name C or name O or name CB )) or resid 406 through 407 o \ r (resid 408 through 409 and (name N or name CA or name C or name O or name CB ) \ ) or resid 410 through 419 or (resid 420 through 422 and (name N or name CA or n \ ame C or name O or name CB )) or resid 423 through 452 or (resid 453 and (name N \ or name CA or name C or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ )) or resid 454 through 458 or (resid 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 through 499 or resid 524 \ through 535 or (resid 536 and (name N or name CA or name C or name O or name CB \ )) or resid 537 through 539 or (resid 540 through 541 and (name N or name CA or \ name C or name O or name CB )) or resid 542 through 543 or (resid 544 through 54 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) or re \ sid 557 through 558 or (resid 559 and (name N or name CA or name C or name O or \ name CB )) or resid 560 or resid 565 or (resid 566 and (name N or name CA or nam \ e C or name O or name CB )) or resid 567 through 574 or (resid 575 and (name N o \ r name CA or name C or name O or name CB )) or resid 576 through 602 or (resid 6 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 604 through \ 616 or (resid 617 through 618 and (name N or name CA or name C or name O or nam \ e CB )) or resid 619 or (resid 620 and (name N or name CA or name C or name O or \ name CB )) or resid 621 through 635 or (resid 636 and (name N or name CA or nam \ e C or name O or name CB )) or resid 637 through 644 or (resid 645 through 646 a \ nd (name N or name CA or name C or name O or name CB )) or resid 647 through 672 \ or resid 678 through 704 or (resid 705 through 707 and (name N or name CA or na \ me C or name O or name CB )) or resid 708 through 709 or resid 711 through 736 o \ r (resid 737 through 738 and (name N or name CA or name C or name O or name CB ) \ ) or resid 739 through 763 or (resid 764 through 765 and (name N or name CA or n \ ame C or name O or name CB )) or resid 766 or (resid 767 and (name N or name CA \ or name C or name O or name CB )) or resid 768 through 775 or (resid 776 through \ 778 and (name N or name CA or name C or name O or name CB )) or resid 779 throu \ gh 783 or (resid 784 through 785 and (name N or name CA or name C or name O or n \ ame CB )) or resid 786 through 825 or (resid 826 and (name N or name CA or name \ C or name O or name CB )) or resid 827 through 828 or resid 839 through 866 or ( \ resid 867 and (name N or name CA or name C or name O or name CB )) or resid 868 \ or resid 873 through 875 or (resid 876 through 878 and (name N or name CA or nam \ e C or name O or name CB )) or resid 879 through 917 or (resid 918 and (name N o \ r name CA or name C or name O or name CB )) or resid 919 through 1031 or (resid \ 1032 and (name N or name CA or name C or name O or name CB )) or resid 1033)) } 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: 1.440 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.930 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.009 0.078 22939 Z= 0.416 Angle : 0.998 10.017 31211 Z= 0.631 Chirality : 0.056 0.374 3755 Planarity : 0.004 0.051 3975 Dihedral : 13.443 89.985 8109 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 1.41 % Allowed : 8.95 % Favored : 89.64 % Rotamer: Outliers : 1.78 % Allowed : 5.29 % Favored : 92.93 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.33 % 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: -2.84 (0.14), residues: 2973 helix: -1.34 (0.13), residues: 1515 sheet: -1.69 (0.27), residues: 370 loop : -2.57 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 185 TYR 0.036 0.002 TYR C 77 PHE 0.037 0.002 PHE C 762 TRP 0.013 0.002 TRP A 634 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.42 (22939) covalent geometry : angle 0.99843 / 0.63 (31211) hydrogen bonds : bond 0.20091 / 13.28 ( 1162) hydrogen bonds : angle 7.98139 / 5.48 ( 3336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 520 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 PHE cc_start: 0.8231 (t80) cc_final: 0.7875 (t80) REVERT: B 407 ASP cc_start: 0.7414 (t0) cc_final: 0.7067 (t0) REVERT: B 437 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: B 438 ILE cc_start: 0.8644 (pt) cc_final: 0.8252 (pt) REVERT: B 573 MET cc_start: 0.8177 (mtp) cc_final: 0.7900 (ttm) REVERT: B 910 ILE cc_start: 0.8087 (mm) cc_final: 0.7735 (mt) REVERT: C 28 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8383 (pp) REVERT: C 121 GLU cc_start: 0.7461 (pm20) cc_final: 0.7253 (pm20) REVERT: C 472 ILE cc_start: 0.8892 (tp) cc_final: 0.8584 (tp) REVERT: C 476 SER cc_start: 0.9250 (p) cc_final: 0.9030 (p) REVERT: C 552 MET cc_start: 0.8748 (ttp) cc_final: 0.8486 (ttp) REVERT: A 120 GLN cc_start: 0.8349 (tp40) cc_final: 0.8132 (tp40) REVERT: A 162 MET cc_start: 0.8800 (ptm) cc_final: 0.8560 (ptm) REVERT: A 414 GLU cc_start: 0.7720 (tt0) cc_final: 0.7425 (tt0) REVERT: A 476 SER cc_start: 0.9110 (m) cc_final: 0.8898 (m) REVERT: A 667 ASN cc_start: 0.8027 (t0) cc_final: 0.7677 (t0) REVERT: A 906 PRO cc_start: 0.8686 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 907 LEU cc_start: 0.8008 (tp) cc_final: 0.7634 (mt) REVERT: A 1008 MET cc_start: 0.8131 (ttm) cc_final: 0.7824 (ttp) REVERT: A 1032 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6701 (tpp-160) outliers start: 42 outliers final: 27 residues processed: 553 average time/residue: 0.1466 time to fit residues: 127.4472 Evaluate side-chains 452 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 423 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 997 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 958 LYS Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.6353 > 50:) chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN B 526 HIS ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 151 GLN C 737 GLN A 181 GLN A 338 HIS A 415 ASN A 697 GLN A 709 HIS A 719 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113289 restraints weight = 33087.119| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.94 r_work: 0.3164 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 22939 Z= 0.164 Angle : 0.684 9.108 31211 Z= 0.353 Chirality : 0.044 0.194 3755 Planarity : 0.005 0.062 3975 Dihedral : 5.632 58.673 3216 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.03 % Allowed : 12.44 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.73 (0.15), residues: 2973 helix: -0.34 (0.13), residues: 1537 sheet: -1.29 (0.27), residues: 387 loop : -2.17 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 518 TYR 0.021 0.002 TYR C 77 PHE 0.020 0.002 PHE A 11 TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (22939) covalent geometry : angle 0.68405 / 0.35 (31211) hydrogen bonds : bond 0.04793 / 3.14 ( 1162) hydrogen bonds : angle 5.31486 / 3.63 ( 3336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 448 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: B 407 ASP cc_start: 0.7359 (t0) cc_final: 0.7098 (t70) REVERT: B 844 MET cc_start: 0.8956 (mmm) cc_final: 0.8715 (mmt) REVERT: B 910 ILE cc_start: 0.7955 (mm) cc_final: 0.7486 (mt) REVERT: C 11 PHE cc_start: 0.8610 (t80) cc_final: 0.8323 (t80) REVERT: C 121 GLU cc_start: 0.7810 (pm20) cc_final: 0.7494 (pm20) REVERT: C 400 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8836 (mp) REVERT: C 472 ILE cc_start: 0.8900 (tp) cc_final: 0.8651 (tp) REVERT: C 552 MET cc_start: 0.8823 (ttp) cc_final: 0.8542 (ttp) REVERT: C 910 ILE cc_start: 0.8558 (tp) cc_final: 0.8311 (tp) REVERT: A 13 TRP cc_start: 0.8494 (m100) cc_final: 0.8151 (m100) REVERT: A 162 MET cc_start: 0.9097 (ptm) cc_final: 0.8880 (ptm) REVERT: A 435 MET cc_start: 0.8411 (tpp) cc_final: 0.8151 (tpt) REVERT: A 667 ASN cc_start: 0.8213 (t0) cc_final: 0.7803 (t0) REVERT: A 828 LEU cc_start: 0.8641 (tp) cc_final: 0.8403 (mp) REVERT: A 906 PRO cc_start: 0.8462 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: A 1008 MET cc_start: 0.8092 (ttm) cc_final: 0.7721 (ttp) REVERT: A 1032 ARG cc_start: 0.7052 (ttm170) cc_final: 0.6430 (tpp-160) outliers start: 48 outliers final: 28 residues processed: 476 average time/residue: 0.1425 time to fit residues: 108.2961 Evaluate side-chains 425 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 396 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1029 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 179 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 81 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 chunk 175 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN B 254 ASN B 274 ASN B 526 HIS C 68 ASN C 737 GLN A 34 GLN A 338 HIS A 415 ASN A 709 HIS A 719 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116014 restraints weight = 33115.614| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.92 r_work: 0.3207 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22939 Z= 0.114 Angle : 0.588 9.617 31211 Z= 0.299 Chirality : 0.041 0.172 3755 Planarity : 0.004 0.054 3975 Dihedral : 4.582 55.826 3177 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.11 % Favored : 94.72 % Rotamer: Outliers : 2.33 % Allowed : 15.74 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.08 (0.15), residues: 2973 helix: 0.22 (0.14), residues: 1520 sheet: -0.96 (0.28), residues: 393 loop : -1.92 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 518 TYR 0.020 0.001 TYR A 35 PHE 0.021 0.001 PHE B 362 TRP 0.009 0.001 TRP B 754 HIS 0.012 0.001 HIS A 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22939) covalent geometry : angle 0.58791 / 0.30 (31211) hydrogen bonds : bond 0.03678 / 2.40 ( 1162) hydrogen bonds : angle 4.84120 / 3.29 ( 3336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 0.597 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash REVERT: B 435 MET cc_start: 0.8805 (tpp) cc_final: 0.8381 (tpt) REVERT: B 536 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.6765 (ptp90) REVERT: B 844 MET cc_start: 0.9011 (mmm) cc_final: 0.8789 (mmt) REVERT: B 899 PHE cc_start: 0.8045 (m-80) cc_final: 0.7756 (m-80) REVERT: C 112 GLN cc_start: 0.8464 (mp10) cc_final: 0.8157 (mp10) REVERT: C 182 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: C 193 LEU cc_start: 0.8389 (pp) cc_final: 0.8120 (mt) REVERT: C 229 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7553 (mm-40) REVERT: C 361 ASN cc_start: 0.8047 (t0) cc_final: 0.7737 (t0) REVERT: C 552 MET cc_start: 0.8736 (ttp) cc_final: 0.8459 (ttp) REVERT: A 13 TRP cc_start: 0.8466 (m100) cc_final: 0.8055 (m100) REVERT: A 162 MET cc_start: 0.9075 (ptm) cc_final: 0.8857 (ptm) REVERT: A 356 TYR cc_start: 0.8378 (t80) cc_final: 0.8157 (t80) REVERT: A 667 ASN cc_start: 0.8090 (t0) cc_final: 0.7798 (t0) REVERT: A 668 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 906 PRO cc_start: 0.8595 (Cg_endo) cc_final: 0.8238 (Cg_exo) REVERT: A 1008 MET cc_start: 0.7966 (ttm) cc_final: 0.7735 (ttp) REVERT: A 1032 ARG cc_start: 0.6995 (ttm170) cc_final: 0.6377 (tpp-160) outliers start: 55 outliers final: 29 residues processed: 456 average time/residue: 0.1396 time to fit residues: 102.3288 Evaluate side-chains 410 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 991 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 149 optimal weight: 5.9990 chunk 80 optimal weight: 0.0020 chunk 179 optimal weight: 0.0570 chunk 261 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS C 89 GLN A 415 ASN A 719 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115793 restraints weight = 33089.180| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.98 r_work: 0.3200 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22939 Z= 0.119 Angle : 0.567 8.946 31211 Z= 0.288 Chirality : 0.041 0.154 3755 Planarity : 0.004 0.053 3975 Dihedral : 4.207 44.877 3172 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.12 % Rotamer: Outliers : 2.45 % Allowed : 17.35 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.78 (0.16), residues: 2973 helix: 0.44 (0.14), residues: 1531 sheet: -0.79 (0.28), residues: 395 loop : -1.78 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 518 TYR 0.023 0.001 TYR A 35 PHE 0.020 0.001 PHE A 918 TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22939) covalent geometry : angle 0.56713 / 0.29 (31211) hydrogen bonds : bond 0.03500 / 2.29 ( 1162) hydrogen bonds : angle 4.62286 / 3.15 ( 3336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 0.766 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 536 ARG cc_start: 0.7527 (ptp-110) cc_final: 0.7018 (ptp90) REVERT: B 844 MET cc_start: 0.9011 (mmm) cc_final: 0.8785 (mmt) REVERT: B 899 PHE cc_start: 0.8061 (m-80) cc_final: 0.7701 (m-80) REVERT: C 182 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: C 193 LEU cc_start: 0.8446 (pp) cc_final: 0.8100 (mt) REVERT: C 229 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7527 (mm-40) REVERT: C 361 ASN cc_start: 0.7929 (t0) cc_final: 0.7626 (t0) REVERT: A 13 TRP cc_start: 0.8471 (m100) cc_final: 0.7971 (m100) REVERT: A 415 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: A 668 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 906 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: A 1032 ARG cc_start: 0.6922 (ttm170) cc_final: 0.6340 (tpp-160) outliers start: 58 outliers final: 35 residues processed: 437 average time/residue: 0.1446 time to fit residues: 101.2354 Evaluate side-chains 418 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 379 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1021 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 219 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS C 941 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113512 restraints weight = 32813.920| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.95 r_work: 0.3165 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22939 Z= 0.166 Angle : 0.587 8.426 31211 Z= 0.300 Chirality : 0.042 0.153 3755 Planarity : 0.004 0.052 3975 Dihedral : 4.134 33.642 3169 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.48 % Rotamer: Outliers : 2.67 % Allowed : 18.28 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.71 (0.16), residues: 2973 helix: 0.50 (0.14), residues: 1548 sheet: -0.76 (0.27), residues: 402 loop : -1.80 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 973 TYR 0.021 0.001 TYR A 35 PHE 0.025 0.001 PHE B 362 TRP 0.007 0.001 TRP B 789 HIS 0.004 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (22939) covalent geometry : angle 0.58667 / 0.30 (31211) hydrogen bonds : bond 0.03838 / 2.51 ( 1162) hydrogen bonds : angle 4.58405 / 3.13 ( 3336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 396 time to evaluate : 0.696 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 536 ARG cc_start: 0.7520 (ptp-110) cc_final: 0.7010 (ptp90) REVERT: B 545 TYR cc_start: 0.8333 (t80) cc_final: 0.8113 (t80) REVERT: B 844 MET cc_start: 0.9051 (mmm) cc_final: 0.8738 (mmt) REVERT: B 897 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6838 (mm) REVERT: B 899 PHE cc_start: 0.8112 (m-80) cc_final: 0.7674 (m-80) REVERT: B 1030 ARG cc_start: 0.8140 (mmp80) cc_final: 0.7865 (mmp80) REVERT: C 89 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8774 (pt0) REVERT: C 182 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: C 229 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7544 (mm-40) REVERT: C 361 ASN cc_start: 0.7926 (t0) cc_final: 0.7623 (t0) REVERT: A 13 TRP cc_start: 0.8548 (m100) cc_final: 0.8118 (m100) REVERT: A 668 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 683 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8449 (mm-30) REVERT: A 1032 ARG cc_start: 0.6963 (ttm170) cc_final: 0.6399 (tpp-160) outliers start: 63 outliers final: 43 residues processed: 434 average time/residue: 0.1417 time to fit residues: 97.9450 Evaluate side-chains 424 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 376 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 991 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114148 restraints weight = 32982.549| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.00 r_work: 0.3175 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22939 Z= 0.140 Angle : 0.577 8.748 31211 Z= 0.293 Chirality : 0.042 0.148 3755 Planarity : 0.004 0.051 3975 Dihedral : 4.084 28.774 3169 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 2.67 % Allowed : 18.49 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.57 (0.16), residues: 2973 helix: 0.60 (0.14), residues: 1554 sheet: -0.66 (0.27), residues: 405 loop : -1.72 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 518 TYR 0.025 0.001 TYR A 35 PHE 0.023 0.001 PHE A 918 TRP 0.008 0.001 TRP A 187 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (22939) covalent geometry : angle 0.57704 / 0.29 (31211) hydrogen bonds : bond 0.03645 / 2.38 ( 1162) hydrogen bonds : angle 4.51339 / 3.07 ( 3336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 381 time to evaluate : 0.864 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 536 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.6990 (ptp90) REVERT: B 545 TYR cc_start: 0.8168 (t80) cc_final: 0.7906 (t80) REVERT: B 844 MET cc_start: 0.9073 (mmm) cc_final: 0.8698 (mmt) REVERT: B 897 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6844 (mm) REVERT: B 899 PHE cc_start: 0.8139 (m-80) cc_final: 0.7704 (m-80) REVERT: B 910 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7606 (mt) REVERT: C 182 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: C 229 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7500 (mm-40) REVERT: C 361 ASN cc_start: 0.7924 (t0) cc_final: 0.7640 (t0) REVERT: C 400 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8903 (mp) REVERT: C 487 ILE cc_start: 0.8726 (mt) cc_final: 0.8426 (pt) REVERT: C 664 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6848 (p90) REVERT: A 13 TRP cc_start: 0.8529 (m100) cc_final: 0.8106 (m100) REVERT: A 435 MET cc_start: 0.8648 (tpt) cc_final: 0.7615 (tpt) REVERT: A 668 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 1032 ARG cc_start: 0.6966 (ttm170) cc_final: 0.6418 (tpp-160) outliers start: 63 outliers final: 45 residues processed: 422 average time/residue: 0.1483 time to fit residues: 100.3289 Evaluate side-chains 417 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 365 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 664 PHE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 991 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 181 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 240 optimal weight: 0.1980 chunk 217 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 179 optimal weight: 0.2980 chunk 222 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 211 optimal weight: 0.3980 chunk 169 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN B 89 GLN B 526 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117053 restraints weight = 32764.972| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22939 Z= 0.100 Angle : 0.538 8.184 31211 Z= 0.271 Chirality : 0.040 0.149 3755 Planarity : 0.004 0.052 3975 Dihedral : 3.807 23.277 3169 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.25 (0.16), residues: 2973 helix: 0.88 (0.14), residues: 1539 sheet: -0.56 (0.28), residues: 401 loop : -1.55 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 259 TYR 0.014 0.001 TYR A 857 PHE 0.031 0.001 PHE A 362 TRP 0.009 0.001 TRP A 187 HIS 0.002 0.000 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (22939) covalent geometry : angle 0.53839 / 0.27 (31211) hydrogen bonds : bond 0.02985 / 1.94 ( 1162) hydrogen bonds : angle 4.33450 / 2.95 ( 3336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 411 time to evaluate : 0.877 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 4 PHE cc_start: 0.8353 (t80) cc_final: 0.8015 (t80) REVERT: B 536 ARG cc_start: 0.7199 (ptp-110) cc_final: 0.6703 (ptp90) REVERT: B 545 TYR cc_start: 0.8101 (t80) cc_final: 0.7789 (t80) REVERT: B 734 GLU cc_start: 0.7242 (tt0) cc_final: 0.6872 (tt0) REVERT: B 844 MET cc_start: 0.9077 (mmm) cc_final: 0.8850 (mmt) REVERT: B 899 PHE cc_start: 0.7861 (m-80) cc_final: 0.7431 (m-80) REVERT: B 910 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7543 (mt) REVERT: C 182 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: C 229 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: C 361 ASN cc_start: 0.7905 (t0) cc_final: 0.7602 (t0) REVERT: C 487 ILE cc_start: 0.8707 (mt) cc_final: 0.8471 (pt) REVERT: C 1032 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6784 (mtm180) REVERT: A 13 TRP cc_start: 0.8389 (m100) cc_final: 0.8081 (m100) REVERT: A 259 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7790 (ptm160) REVERT: A 407 ASP cc_start: 0.8612 (m-30) cc_final: 0.8122 (m-30) REVERT: A 435 MET cc_start: 0.8561 (tpt) cc_final: 0.8315 (tpt) REVERT: A 657 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7613 (mm-40) REVERT: A 1032 ARG cc_start: 0.6949 (ttm170) cc_final: 0.6353 (tpp-160) outliers start: 55 outliers final: 30 residues processed: 446 average time/residue: 0.1393 time to fit residues: 100.8823 Evaluate side-chains 406 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 862 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 215 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 268 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS A 604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114864 restraints weight = 32666.109| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.97 r_work: 0.3188 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22939 Z= 0.134 Angle : 0.570 8.060 31211 Z= 0.289 Chirality : 0.042 0.186 3755 Planarity : 0.004 0.051 3975 Dihedral : 3.840 23.956 3168 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 2.20 % Allowed : 19.97 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.21 (0.16), residues: 2973 helix: 0.92 (0.14), residues: 1541 sheet: -0.53 (0.29), residues: 382 loop : -1.54 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 518 TYR 0.026 0.001 TYR A 35 PHE 0.020 0.001 PHE C 362 TRP 0.006 0.001 TRP B 789 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (22939) covalent geometry : angle 0.56965 / 0.29 (31211) hydrogen bonds : bond 0.03381 / 2.21 ( 1162) hydrogen bonds : angle 4.31841 / 2.94 ( 3336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 382 time to evaluate : 0.816 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: B 298 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8357 (p0) REVERT: B 536 ARG cc_start: 0.7177 (ptp-110) cc_final: 0.6664 (ptp90) REVERT: B 545 TYR cc_start: 0.8115 (t80) cc_final: 0.7841 (t80) REVERT: B 734 GLU cc_start: 0.7318 (tt0) cc_final: 0.6927 (tt0) REVERT: B 844 MET cc_start: 0.9096 (mmm) cc_final: 0.8850 (mmt) REVERT: B 899 PHE cc_start: 0.7935 (m-80) cc_final: 0.7496 (m-80) REVERT: B 910 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7644 (mt) REVERT: C 182 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: C 229 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7500 (mm-40) REVERT: C 361 ASN cc_start: 0.7928 (t0) cc_final: 0.7631 (t0) REVERT: C 487 ILE cc_start: 0.8749 (mt) cc_final: 0.8486 (pt) REVERT: C 664 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.6894 (p90) REVERT: C 817 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: C 987 MET cc_start: 0.8035 (mtp) cc_final: 0.7612 (mmp) REVERT: C 1031 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6649 (ptp90) REVERT: C 1032 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6830 (mtm180) REVERT: A 259 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7798 (ptm160) REVERT: A 407 ASP cc_start: 0.8675 (m-30) cc_final: 0.8138 (m-30) REVERT: A 435 MET cc_start: 0.8616 (tpt) cc_final: 0.8303 (tpt) REVERT: A 657 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7621 (mm-40) REVERT: A 1032 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6470 (tpp-160) outliers start: 52 outliers final: 38 residues processed: 416 average time/residue: 0.1398 time to fit residues: 94.4734 Evaluate side-chains 412 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 664 PHE Chi-restraints excluded: chain C residue 774 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 862 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 179 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 0.0370 chunk 153 optimal weight: 6.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112183 restraints weight = 33055.422| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.97 r_work: 0.3145 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22939 Z= 0.185 Angle : 0.611 7.806 31211 Z= 0.312 Chirality : 0.043 0.165 3755 Planarity : 0.004 0.051 3975 Dihedral : 4.086 24.432 3168 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 2.33 % Allowed : 20.02 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.32 (0.16), residues: 2973 helix: 0.82 (0.14), residues: 1551 sheet: -0.58 (0.28), residues: 393 loop : -1.62 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 259 TYR 0.022 0.001 TYR A 327 PHE 0.017 0.001 PHE C 362 TRP 0.007 0.001 TRP A 187 HIS 0.004 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (22939) covalent geometry : angle 0.61121 / 0.31 (31211) hydrogen bonds : bond 0.03983 / 2.59 ( 1162) hydrogen bonds : angle 4.44845 / 3.04 ( 3336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 376 time to evaluate : 0.891 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash REVERT: B 4 PHE cc_start: 0.8315 (t80) cc_final: 0.7961 (t80) REVERT: B 298 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8365 (p0) REVERT: B 545 TYR cc_start: 0.8151 (t80) cc_final: 0.7856 (t80) REVERT: B 897 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6811 (mm) REVERT: B 899 PHE cc_start: 0.8134 (m-80) cc_final: 0.7633 (m-80) REVERT: B 910 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (mt) REVERT: C 182 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: C 229 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: C 322 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8638 (ttmm) REVERT: C 361 ASN cc_start: 0.7948 (t0) cc_final: 0.7667 (t0) REVERT: C 662 MET cc_start: 0.8284 (tpp) cc_final: 0.8060 (ttm) REVERT: C 664 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6974 (p90) REVERT: C 987 MET cc_start: 0.7975 (mtp) cc_final: 0.7516 (mmp) REVERT: C 1032 ARG cc_start: 0.7466 (mtt180) cc_final: 0.6922 (mtm180) REVERT: A 435 MET cc_start: 0.8638 (tpt) cc_final: 0.8266 (tpt) REVERT: A 1032 ARG cc_start: 0.6974 (ttm170) cc_final: 0.6502 (tpp-160) outliers start: 55 outliers final: 43 residues processed: 413 average time/residue: 0.1433 time to fit residues: 95.2150 Evaluate side-chains 420 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 664 PHE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 196 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113367 restraints weight = 32958.834| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.98 r_work: 0.3165 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22939 Z= 0.142 Angle : 0.587 9.088 31211 Z= 0.298 Chirality : 0.042 0.171 3755 Planarity : 0.004 0.051 3975 Dihedral : 4.034 24.413 3168 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 2.12 % Allowed : 20.57 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2973 helix: 0.86 (0.14), residues: 1551 sheet: -0.47 (0.28), residues: 401 loop : -1.58 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 518 TYR 0.018 0.001 TYR A 327 PHE 0.018 0.001 PHE A 664 TRP 0.009 0.001 TRP A 187 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (22939) covalent geometry : angle 0.58654 / 0.30 (31211) hydrogen bonds : bond 0.03646 / 2.38 ( 1162) hydrogen bonds : angle 4.40346 / 3.00 ( 3336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 368 time to evaluate : 0.888 Fit side-chains Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash REVERT: B 4 PHE cc_start: 0.8256 (t80) cc_final: 0.7897 (t80) REVERT: B 518 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7853 (mtm-85) REVERT: B 545 TYR cc_start: 0.8101 (t80) cc_final: 0.7837 (t80) REVERT: B 897 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6885 (mm) REVERT: B 899 PHE cc_start: 0.8107 (m-80) cc_final: 0.7614 (m-80) REVERT: C 182 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: C 229 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7400 (mm-40) REVERT: C 322 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8623 (ttmm) REVERT: C 361 ASN cc_start: 0.7892 (t0) cc_final: 0.7615 (t0) REVERT: C 487 ILE cc_start: 0.8781 (mt) cc_final: 0.8463 (pt) REVERT: C 662 MET cc_start: 0.8269 (tpp) cc_final: 0.8068 (ttm) REVERT: C 664 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7040 (p90) REVERT: C 987 MET cc_start: 0.7991 (mtp) cc_final: 0.7551 (mmp) REVERT: C 1032 ARG cc_start: 0.7495 (mtt180) cc_final: 0.6861 (mtm180) REVERT: A 435 MET cc_start: 0.8616 (tpt) cc_final: 0.8257 (tpt) REVERT: A 657 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7606 (mm-40) REVERT: A 1032 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6501 (tpp-160) outliers start: 50 outliers final: 43 residues processed: 405 average time/residue: 0.1411 time to fit residues: 92.6631 Evaluate side-chains 411 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 664 PHE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 259 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 810 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 61 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 ASN B 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110931 restraints weight = 33160.865| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.00 r_work: 0.3125 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22939 Z= 0.222 Angle : 0.639 7.690 31211 Z= 0.327 Chirality : 0.045 0.180 3755 Planarity : 0.004 0.054 3975 Dihedral : 4.239 24.366 3168 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.07 % Allowed : 20.48 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.41 (0.16), residues: 2973 helix: 0.75 (0.13), residues: 1549 sheet: -0.60 (0.28), residues: 391 loop : -1.65 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 518 TYR 0.026 0.002 TYR C 527 PHE 0.017 0.002 PHE A 918 TRP 0.008 0.001 TRP B 13 HIS 0.005 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.22 (22939) covalent geometry : angle 0.63945 / 0.33 (31211) hydrogen bonds : bond 0.04240 / 2.77 ( 1162) hydrogen bonds : angle 4.53891 / 3.10 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5912.36 seconds wall clock time: 101 minutes 55.06 seconds (6115.06 seconds total)