Starting phenix.real_space_refine on Sun Aug 24 22:08:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.map" model { file = "/net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yr0_39532/08_2025/8yr0_39532.cif" } resolution = 3.06 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= 0.012 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 88 5.16 5 C 14954 2.51 5 N 3887 2.21 5 O 4199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23128 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7645 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 136 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7638 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 4 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 138 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 10, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 7644 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 4 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 7, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 6.07, per 1000 atoms: 0.26 Number of scatterers: 23128 At special positions: 0 Unit cell: (122.12, 120.4, 138.46, 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 88 16.00 O 4199 8.00 N 3887 7.00 C 14954 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 23 sheets defined 59.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.580A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 7 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 removed outlier: 3.729A pdb=" N ALA A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.891A pdb=" N LEU A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 115 through 120 Proline residue: A 118 - end of helix No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 152 through 170 removed outlier: 3.575A pdb=" N ASN A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.565A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 331 through 361 removed outlier: 3.669A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 387 removed outlier: 4.142A pdb=" N LEU A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 4.580A pdb=" N PHE A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 4.020A pdb=" N ILE A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.893A pdb=" N GLU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 458 Processing helix chain 'A' and resid 461 through 497 removed outlier: 4.629A pdb=" N GLN A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 505 through 515 removed outlier: 3.529A pdb=" N ILE A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 541 Processing helix chain 'A' and resid 543 through 565 removed outlier: 3.758A pdb=" N GLY A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.569A pdb=" N THR A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 697 through 714 removed outlier: 3.803A pdb=" N LEU A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.896A pdb=" N MET A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 786 removed outlier: 4.149A pdb=" N ALA A 786 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.942A pdb=" N ILE A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 857 removed outlier: 3.793A pdb=" N GLU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 855 " --> pdb=" O ARG A 851 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 876 Processing helix chain 'A' and resid 881 through 899 Processing helix chain 'A' and resid 902 through 909 removed outlier: 4.271A pdb=" N ALA A 906 " --> pdb=" O THR A 902 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 removed outlier: 3.768A pdb=" N ILE A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 962 removed outlier: 3.543A pdb=" N GLY A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 976 removed outlier: 3.621A pdb=" N ARG A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 removed outlier: 3.611A pdb=" N ILE A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 996 removed outlier: 3.606A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1039 removed outlier: 3.998A pdb=" N MET A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A1027 " --> pdb=" O GLY A1023 " (cutoff:3.500A) Proline residue: A1028 - end of helix Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.714A pdb=" N PHE B 7 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.638A pdb=" N ALA B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 63 through 72 removed outlier: 3.844A pdb=" N LEU B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 115 through 120 Proline residue: B 118 - end of helix No H-bonds generated for 'chain 'B' and resid 115 through 120' Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.605A pdb=" N LEU B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.287A pdb=" N LYS B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.566A pdb=" N VAL B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 331 through 360 removed outlier: 3.760A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 367 through 388 Proline residue: B 374 - end of helix removed outlier: 4.420A pdb=" N PHE B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 425 removed outlier: 4.965A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.835A pdb=" N GLU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 461 through 497 removed outlier: 4.579A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 505 through 543 removed outlier: 6.867A pdb=" N ARG B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 562 removed outlier: 3.538A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 606 removed outlier: 3.762A pdb=" N THR B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 648 Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 697 through 714 Processing helix chain 'B' and resid 747 through 759 removed outlier: 3.576A pdb=" N THR B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.190A pdb=" N ALA B 786 " --> pdb=" O PRO B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 removed outlier: 3.836A pdb=" N ILE B 791 " --> pdb=" O PRO B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 857 Processing helix chain 'B' and resid 866 through 875 Processing helix chain 'B' and resid 878 through 880 No H-bonds generated for 'chain 'B' and resid 878 through 880' Processing helix chain 'B' and resid 881 through 898 removed outlier: 3.665A pdb=" N ILE B 885 " --> pdb=" O TRP B 881 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 909 removed outlier: 4.101A pdb=" N ALA B 906 " --> pdb=" O THR B 902 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 925 removed outlier: 3.886A pdb=" N ILE B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 935 Processing helix chain 'B' and resid 936 through 962 removed outlier: 4.174A pdb=" N LEU B 940 " --> pdb=" O GLY B 936 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 951 " --> pdb=" O ASN B 947 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 976 removed outlier: 3.510A pdb=" N ARG B 976 " --> pdb=" O ALA B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.792A pdb=" N ILE B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 996 removed outlier: 3.537A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1026 removed outlier: 4.184A pdb=" N ALA B1007 " --> pdb=" O GLU B1003 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B1008 " --> pdb=" O MET B1004 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY B1018 " --> pdb=" O PHE B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1039 Processing helix chain 'C' and resid 3 through 9 removed outlier: 3.765A pdb=" N PHE C 7 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 9 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 30 removed outlier: 3.693A pdb=" N ALA C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 63 Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.989A pdb=" N LEU C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.646A pdb=" N GLN C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.531A pdb=" N LEU C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 removed outlier: 3.559A pdb=" N ARG C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.558A pdb=" N ARG C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 299 through 316 removed outlier: 3.813A pdb=" N LYS C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 361 removed outlier: 3.832A pdb=" N ARG C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.758A pdb=" N LEU C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 388 removed outlier: 3.513A pdb=" N ILE C 377 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 382 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 424 removed outlier: 4.370A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.802A pdb=" N GLU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 497 removed outlier: 4.538A pdb=" N GLN C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 505 through 515 Processing helix chain 'C' and resid 517 through 543 removed outlier: 3.608A pdb=" N SER C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 562 Processing helix chain 'C' and resid 589 through 606 removed outlier: 3.737A pdb=" N THR C 593 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 648 Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 697 through 715 removed outlier: 3.672A pdb=" N SER C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 715 " --> pdb=" O ALA C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 760 Processing helix chain 'C' and resid 782 through 786 removed outlier: 4.172A pdb=" N ALA C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 removed outlier: 3.592A pdb=" N ILE C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 857 Processing helix chain 'C' and resid 866 through 876 removed outlier: 3.503A pdb=" N TYR C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 880 No H-bonds generated for 'chain 'C' and resid 878 through 880' Processing helix chain 'C' and resid 881 through 899 Processing helix chain 'C' and resid 904 through 909 removed outlier: 3.762A pdb=" N LEU C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 removed outlier: 3.863A pdb=" N ILE C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 917 " --> pdb=" O MET C 913 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 921 " --> pdb=" O ALA C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 961 removed outlier: 3.956A pdb=" N LEU C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET C 938 " --> pdb=" O GLN C 934 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 940 " --> pdb=" O GLY C 936 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 975 Processing helix chain 'C' and resid 976 through 991 removed outlier: 3.656A pdb=" N ILE C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 996 removed outlier: 3.523A pdb=" N VAL C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1039 removed outlier: 4.525A pdb=" N ALA C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N MET C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C1021 " --> pdb=" O ILE C1017 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C1024 " --> pdb=" O THR C1020 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C1027 " --> pdb=" O GLY C1023 " (cutoff:3.500A) Proline residue: C1028 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.920A pdb=" N ASN A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 95 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR A 79 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL A 822 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.920A pdb=" N ASN A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 95 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR A 79 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL A 822 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR A 828 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 692 " --> pdb=" O THR A 828 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.826A pdb=" N GLU A 176 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 140 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN A 294 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 138 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 141 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 327 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.826A pdb=" N GLU A 176 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 632 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 630 " --> pdb=" O GLY A 618 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 273 removed outlier: 7.794A pdb=" N TYR A 185 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN A 775 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 776 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 765 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA A 778 " --> pdb=" O TYR A 763 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A 763 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 236 removed outlier: 6.127A pdb=" N SER A 234 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 734 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 236 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N LEU B 736 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.998A pdb=" N THR A 261 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 810 through 817 Processing sheet with id=AA9, first strand: chain 'A' and resid 795 through 797 Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.892A pdb=" N TYR B 79 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL B 822 " --> pdb=" O SER B 829 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.892A pdb=" N TYR B 79 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL B 822 " --> pdb=" O SER B 829 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR B 828 " --> pdb=" O ASP B 692 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 692 " --> pdb=" O THR B 828 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.975A pdb=" N VAL B 141 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 632 " --> pdb=" O PHE B 616 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 630 " --> pdb=" O GLY B 618 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 273 removed outlier: 7.580A pdb=" N TYR B 185 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN B 775 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG B 772 " --> pdb=" O ASN B 768 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 768 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR B 774 " --> pdb=" O ASP B 766 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP B 766 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 776 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.878A pdb=" N GLY B 220 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER B 234 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL C 734 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 236 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N LEU C 736 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 253 removed outlier: 7.010A pdb=" N THR B 261 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 795 through 797 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.708A pdb=" N TYR C 79 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL C 822 " --> pdb=" O SER C 829 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.708A pdb=" N TYR C 79 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL C 822 " --> pdb=" O SER C 829 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR C 828 " --> pdb=" O ASP C 692 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 174 through 177 removed outlier: 4.387A pdb=" N GLU C 176 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 140 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN C 294 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 138 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 141 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 327 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 273 removed outlier: 7.498A pdb=" N TYR C 185 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN C 775 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 776 " --> pdb=" O ASN C 765 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN C 765 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA C 778 " --> pdb=" O TYR C 763 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C 763 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 251 through 253 removed outlier: 7.078A pdb=" N THR C 261 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.626A pdb=" N ILE C 632 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 630 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 795 through 796 1502 hydrogen bonds defined for protein. 4317 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: 5.93 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7455 1.35 - 1.47: 5320 1.47 - 1.59: 10621 1.59 - 1.71: 0 1.71 - 1.83: 173 Bond restraints: 23569 Sorted by residual: bond pdb=" C3' LMT B1101 " pdb=" O3' LMT B1101 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C6' LMT C1101 " pdb=" O6' LMT C1101 " ideal model delta sigma weight residual 1.407 1.366 0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C3' LMT A1101 " pdb=" O3' LMT A1101 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C3' LMT C1101 " pdb=" O3' LMT C1101 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C7 LMT A1102 " pdb=" C8 LMT A1102 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 23564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 31539 1.97 - 3.95: 455 3.95 - 5.92: 109 5.92 - 7.89: 25 7.89 - 9.87: 17 Bond angle restraints: 32145 Sorted by residual: angle pdb=" N VAL C 40 " pdb=" CA VAL C 40 " pdb=" C VAL C 40 " ideal model delta sigma weight residual 113.53 109.64 3.89 9.80e-01 1.04e+00 1.58e+01 angle pdb=" C PHE A1025 " pdb=" N LEU A1026 " pdb=" CA LEU A1026 " ideal model delta sigma weight residual 121.54 114.52 7.02 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C2 LMT A1101 " pdb=" C3 LMT A1101 " pdb=" C4 LMT A1101 " ideal model delta sigma weight residual 117.09 107.22 9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 111.90 109.25 2.65 8.10e-01 1.52e+00 1.07e+01 angle pdb=" C2 LMT A1102 " pdb=" C3 LMT A1102 " pdb=" C4 LMT A1102 " ideal model delta sigma weight residual 117.09 107.31 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 32140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.48: 13128 25.48 - 50.96: 1014 50.96 - 76.44: 113 76.44 - 101.92: 42 101.92 - 127.40: 30 Dihedral angle restraints: 14327 sinusoidal: 5429 harmonic: 8898 Sorted by residual: dihedral pdb=" CA MET B 140 " pdb=" C MET B 140 " pdb=" N VAL B 141 " pdb=" CA VAL B 141 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" C2B LMT A1102 " pdb=" C1B LMT A1102 " pdb=" O5B LMT A1102 " pdb=" C5B LMT A1102 " ideal model delta sinusoidal sigma weight residual -57.12 70.28 -127.40 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C2B LMT C1102 " pdb=" C1B LMT C1102 " pdb=" O5B LMT C1102 " pdb=" C5B LMT C1102 " ideal model delta sinusoidal sigma weight residual -57.12 70.24 -127.36 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 14324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3258 0.055 - 0.109: 605 0.109 - 0.164: 59 0.164 - 0.219: 17 0.219 - 0.273: 3 Chirality restraints: 3942 Sorted by residual: chirality pdb=" C5' LMT B1102 " pdb=" C4' LMT B1102 " pdb=" C6' LMT B1102 " pdb=" O5' LMT B1102 " both_signs ideal model delta sigma weight residual False -2.51 -2.23 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5' LMT C1102 " pdb=" C4' LMT C1102 " pdb=" C6' LMT C1102 " pdb=" O5' LMT C1102 " both_signs ideal model delta sigma weight residual False -2.51 -2.24 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5' LMT A1102 " pdb=" C4' LMT A1102 " pdb=" C6' LMT A1102 " pdb=" O5' LMT A1102 " both_signs ideal model delta sigma weight residual False -2.51 -2.24 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3939 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 290 " 0.047 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 291 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 329 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO C 330 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 329 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 330 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.035 5.00e-02 4.00e+02 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1816 2.74 - 3.28: 22776 3.28 - 3.82: 36811 3.82 - 4.36: 38927 4.36 - 4.90: 72428 Nonbonded interactions: 172758 Sorted by model distance: nonbonded pdb=" OG SER C 612 " pdb=" OG1 THR C 636 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR C 763 " pdb=" OD1 ASP C 766 " model vdw 2.260 3.040 nonbonded pdb=" NE2 GLN A 576 " pdb=" O LEU A 637 " model vdw 2.290 3.120 nonbonded pdb=" NE2 GLN C 576 " pdb=" O LEU C 637 " model vdw 2.301 3.120 nonbonded pdb=" NH1 ARG A 279 " pdb=" OE1 GLU A 594 " model vdw 2.316 3.120 ... (remaining 172753 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 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 328 or (resid 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 428 or (resid 429 t \ hrough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ through 645 or (resid 646 through 647 and (name N or name CA or name C or name \ O or name CB )) or resid 648 through 712 or (resid 713 and (name N or name CA or \ name C or name O or name CB )) or resid 714 through 734 or (resid 735 and (name \ N or name CA or name C or name O or name CB )) or resid 736 through 749 or (res \ id 750 and (name N or name CA or name C or name O or name CB )) or resid 751 thr \ ough 788 or (resid 789 and (name N or name CA or name C or name O or name CB )) \ or resid 790 through 843 or (resid 844 through 848 and (name N or name CA or nam \ e C or name O or name CB )) or resid 849 through 854 or (resid 855 and (name N o \ r name CA or name C or name O or name CB )) or resid 856 through 898 or (resid 8 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 900 through \ 927 or (resid 928 and (name N or name CA or name C or name O or name CB )) or r \ esid 929 through 952 or (resid 953 and (name N or name CA or name C or name O or \ name CB )) or resid 954 through 1002 or (resid 1003 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1004 through 1102)) selection = (chain 'B' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 96 or (resid 97 and (n \ ame N or name CA or name C or name O or name CB )) or resid 98 through 102 or (r \ esid 103 through 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 110 or (resid 111 and (name N or name CA or name C or name O \ or name CB )) or resid 112 through 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB )) or resid 115 through 122 or (resid 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 132 or (resid \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throu \ gh 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or \ resid 149 through 243 or (resid 244 and (name N or name CA or name C or name O \ or name CB )) or resid 245 through 712 or (resid 713 and (name N or name CA or n \ ame C or name O or name CB )) or resid 714 through 788 or (resid 789 and (name N \ or name CA or name C or name O or name CB )) or resid 790 through 819 or (resid \ 820 and (name N or name CA or name C or name O or name CB )) or resid 821 throu \ gh 898 or (resid 899 and (name N or name CA or name C or name O or name CB )) or \ resid 900 through 1002 or (resid 1003 and (name N or name CA or name C or name \ O or name CB )) or resid 1004 through 1102)) selection = (chain 'C' and (resid 2 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 110 or (resid 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 113 or (resid 114 a \ nd (name N or name CA or name C or name O or name CB )) or resid 115 through 132 \ or (resid 133 and (name N or name CA or name C or name O or name CB )) or resid \ 134 through 147 or (resid 148 and (name N or name CA or name C or name O or nam \ e CB )) or resid 149 through 165 or (resid 166 through 167 and (name N or name C \ A or name C or name O or name CB )) or resid 168 through 312 or (resid 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 316 or \ (resid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 \ through 328 or (resid 329 and (name N or name CA or name C or name O or name CB \ )) or resid 330 through 421 or (resid 422 through 423 and (name N or name CA or \ name C or name O or name CB )) or resid 424 through 734 or (resid 735 and (name \ N or name CA or name C or name O or name CB )) or resid 736 through 749 or (res \ id 750 and (name N or name CA or name C or name O or name CB )) or resid 751 thr \ ough 843 or (resid 844 through 848 and (name N or name CA or name C or name O or \ name CB )) or resid 849 through 871 or (resid 872 and (name N or name CA or nam \ e C or name O or name CB )) or resid 873 through 952 or (resid 953 and (name N o \ r name CA or name C or name O or name CB )) or resid 954 through 956 or (resid 9 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 958 through \ 1102)) } 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: 12.000 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.950 Find NCS groups from input model: 0.460 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23569 Z= 0.176 Angle : 0.669 9.866 32145 Z= 0.337 Chirality : 0.043 0.273 3942 Planarity : 0.005 0.073 4070 Dihedral : 18.957 127.403 8591 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.13 % Allowed : 30.44 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3054 helix: 1.52 (0.13), residues: 1641 sheet: 0.65 (0.26), residues: 420 loop : -0.93 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 126 TYR 0.018 0.001 TYR C 155 PHE 0.019 0.001 PHE A1021 TRP 0.012 0.001 TRP B 881 HIS 0.002 0.001 HIS B1006 Details of bonding type rmsd covalent geometry : bond 0.00353 (23569) covalent geometry : angle 0.66879 (32145) hydrogen bonds : bond 0.14008 ( 1435) hydrogen bonds : angle 5.39858 ( 4317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.986 Fit side-chains REVERT: B 414 VAL cc_start: 0.7052 (t) cc_final: 0.6760 (p) outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.1360 time to fit residues: 35.6187 Evaluate side-chains 128 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 411 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 55 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN C 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054734 restraints weight = 68060.538| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.79 r_work: 0.2812 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23569 Z= 0.161 Angle : 0.612 9.173 32145 Z= 0.301 Chirality : 0.045 0.352 3942 Planarity : 0.005 0.051 4070 Dihedral : 9.786 86.109 3659 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.27 % Allowed : 26.91 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.15), residues: 3054 helix: 1.78 (0.13), residues: 1665 sheet: 1.21 (0.26), residues: 384 loop : -1.08 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.015 0.001 TYR C 898 PHE 0.020 0.001 PHE B 397 TRP 0.015 0.001 TRP C 881 HIS 0.002 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00373 (23569) covalent geometry : angle 0.61158 (32145) hydrogen bonds : bond 0.05019 ( 1435) hydrogen bonds : angle 3.88969 ( 4317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 129 time to evaluate : 1.021 Fit side-chains REVERT: A 717 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: B 989 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: B 1016 MET cc_start: 0.9027 (tpt) cc_final: 0.8690 (tpt) outliers start: 78 outliers final: 36 residues processed: 202 average time/residue: 0.1280 time to fit residues: 45.9172 Evaluate side-chains 152 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 755 MET Chi-restraints excluded: chain B residue 989 MET Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 259 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN B 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054745 restraints weight = 67825.606| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.75 r_work: 0.2810 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23569 Z= 0.125 Angle : 0.542 9.496 32145 Z= 0.270 Chirality : 0.042 0.280 3942 Planarity : 0.004 0.050 4070 Dihedral : 6.664 59.095 3657 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.77 % Allowed : 27.62 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.16), residues: 3054 helix: 2.10 (0.13), residues: 1665 sheet: 0.69 (0.24), residues: 468 loop : -0.95 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.016 0.001 TYR B 467 PHE 0.013 0.001 PHE B 932 TRP 0.007 0.001 TRP B 190 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00282 (23569) covalent geometry : angle 0.54199 (32145) hydrogen bonds : bond 0.04491 ( 1435) hydrogen bonds : angle 3.67220 ( 4317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 123 time to evaluate : 0.870 Fit side-chains REVERT: A 359 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7284 (t80) REVERT: A 717 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: C 359 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 66 outliers final: 32 residues processed: 182 average time/residue: 0.1148 time to fit residues: 36.9476 Evaluate side-chains 145 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 910 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 157 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 273 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN B 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.050745 restraints weight = 68397.891| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.12 r_work: 0.2676 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23569 Z= 0.164 Angle : 0.584 9.994 32145 Z= 0.295 Chirality : 0.044 0.330 3942 Planarity : 0.005 0.051 4070 Dihedral : 5.848 58.716 3657 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.27 % Allowed : 27.04 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.16), residues: 3054 helix: 2.12 (0.13), residues: 1668 sheet: 0.99 (0.25), residues: 438 loop : -1.02 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.016 0.001 TYR C 276 PHE 0.017 0.001 PHE B 397 TRP 0.011 0.001 TRP C 190 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00391 (23569) covalent geometry : angle 0.58394 (32145) hydrogen bonds : bond 0.05599 ( 1435) hydrogen bonds : angle 3.76421 ( 4317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 111 time to evaluate : 0.923 Fit side-chains REVERT: A 717 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: B 1016 MET cc_start: 0.8746 (tpt) cc_final: 0.8406 (tpt) REVERT: C 150 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8382 (ttt180) REVERT: C 994 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8249 (mp) outliers start: 78 outliers final: 56 residues processed: 185 average time/residue: 0.1239 time to fit residues: 38.9684 Evaluate side-chains 164 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 105 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 20 optimal weight: 0.6980 chunk 229 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052669 restraints weight = 68164.597| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.75 r_work: 0.2753 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23569 Z= 0.116 Angle : 0.515 9.660 32145 Z= 0.260 Chirality : 0.041 0.219 3942 Planarity : 0.004 0.050 4070 Dihedral : 5.333 59.498 3657 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.90 % Allowed : 27.54 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.16), residues: 3054 helix: 2.32 (0.13), residues: 1659 sheet: 0.81 (0.25), residues: 465 loop : -0.91 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 436 TYR 0.012 0.001 TYR B 467 PHE 0.013 0.001 PHE B 397 TRP 0.007 0.001 TRP C 190 HIS 0.001 0.000 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00261 (23569) covalent geometry : angle 0.51454 (32145) hydrogen bonds : bond 0.04521 ( 1435) hydrogen bonds : angle 3.60884 ( 4317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 105 time to evaluate : 0.812 Fit side-chains REVERT: A 359 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 721 MET cc_start: 0.8518 (mmm) cc_final: 0.8133 (mmm) REVERT: C 989 MET cc_start: 0.9092 (tpp) cc_final: 0.8663 (tpt) REVERT: C 994 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8577 (mp) outliers start: 69 outliers final: 42 residues processed: 172 average time/residue: 0.1236 time to fit residues: 37.2249 Evaluate side-chains 147 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 228 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 269 optimal weight: 0.0270 chunk 258 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 744 GLN A 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053835 restraints weight = 68134.703| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.77 r_work: 0.2778 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23569 Z= 0.101 Angle : 0.492 9.300 32145 Z= 0.248 Chirality : 0.040 0.188 3942 Planarity : 0.004 0.053 4070 Dihedral : 4.839 58.656 3657 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.56 % Allowed : 27.54 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.16), residues: 3054 helix: 2.43 (0.13), residues: 1656 sheet: 0.90 (0.25), residues: 462 loop : -0.86 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 126 TYR 0.014 0.001 TYR B 467 PHE 0.012 0.001 PHE B 397 TRP 0.006 0.001 TRP C 190 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00219 (23569) covalent geometry : angle 0.49188 (32145) hydrogen bonds : bond 0.03834 ( 1435) hydrogen bonds : angle 3.44627 ( 4317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 105 time to evaluate : 0.849 Fit side-chains REVERT: A 158 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8522 (m-40) REVERT: A 359 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 399 MET cc_start: 0.9017 (ttm) cc_final: 0.8791 (mtt) REVERT: B 721 MET cc_start: 0.8485 (mmm) cc_final: 0.8135 (mmm) REVERT: C 144 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (tt) REVERT: C 989 MET cc_start: 0.9079 (tpp) cc_final: 0.8680 (tpt) REVERT: C 994 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8594 (mp) outliers start: 61 outliers final: 46 residues processed: 165 average time/residue: 0.1174 time to fit residues: 34.2642 Evaluate side-chains 153 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 120 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 223 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.053236 restraints weight = 68558.327| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.79 r_work: 0.2762 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23569 Z= 0.109 Angle : 0.495 9.701 32145 Z= 0.249 Chirality : 0.040 0.173 3942 Planarity : 0.004 0.052 4070 Dihedral : 4.763 57.706 3657 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 26.99 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.16), residues: 3054 helix: 2.45 (0.13), residues: 1656 sheet: 0.83 (0.25), residues: 465 loop : -0.81 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.012 0.001 TYR A 185 PHE 0.017 0.001 PHE B 397 TRP 0.006 0.001 TRP C 190 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00247 (23569) covalent geometry : angle 0.49476 (32145) hydrogen bonds : bond 0.04056 ( 1435) hydrogen bonds : angle 3.45906 ( 4317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 106 time to evaluate : 0.873 Fit side-chains REVERT: A 359 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7155 (t80) REVERT: A 399 MET cc_start: 0.9090 (ttm) cc_final: 0.8879 (mtt) REVERT: B 721 MET cc_start: 0.8493 (mmm) cc_final: 0.8125 (mmm) REVERT: C 827 TYR cc_start: 0.8795 (m-80) cc_final: 0.8353 (m-80) REVERT: C 989 MET cc_start: 0.9144 (tpp) cc_final: 0.8754 (tpt) REVERT: C 994 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8687 (mp) outliers start: 71 outliers final: 53 residues processed: 173 average time/residue: 0.1179 time to fit residues: 36.1428 Evaluate side-chains 160 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 2 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 192 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051889 restraints weight = 68231.397| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.75 r_work: 0.2729 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23569 Z= 0.129 Angle : 0.514 10.024 32145 Z= 0.261 Chirality : 0.041 0.179 3942 Planarity : 0.004 0.052 4070 Dihedral : 4.756 59.063 3657 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.94 % Allowed : 26.70 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.16), residues: 3054 helix: 2.46 (0.13), residues: 1659 sheet: 0.83 (0.25), residues: 465 loop : -0.85 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 978 TYR 0.013 0.001 TYR B 467 PHE 0.019 0.001 PHE C 932 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00304 (23569) covalent geometry : angle 0.51433 (32145) hydrogen bonds : bond 0.04719 ( 1435) hydrogen bonds : angle 3.53732 ( 4317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 101 time to evaluate : 0.827 Fit side-chains REVERT: A 359 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 399 MET cc_start: 0.9063 (ttm) cc_final: 0.8813 (mtt) REVERT: A 459 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: A 544 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5923 (mtmt) REVERT: C 994 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 70 outliers final: 56 residues processed: 167 average time/residue: 0.1374 time to fit residues: 39.3221 Evaluate side-chains 160 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 100 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 105 optimal weight: 0.0970 chunk 285 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052177 restraints weight = 68417.798| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.80 r_work: 0.2735 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23569 Z= 0.118 Angle : 0.502 9.470 32145 Z= 0.254 Chirality : 0.040 0.173 3942 Planarity : 0.004 0.052 4070 Dihedral : 4.627 57.019 3657 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.77 % Allowed : 26.99 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.16), residues: 3054 helix: 2.46 (0.13), residues: 1659 sheet: 0.82 (0.25), residues: 465 loop : -0.82 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.011 0.001 TYR B 467 PHE 0.015 0.001 PHE B 397 TRP 0.007 0.001 TRP A 190 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00273 (23569) covalent geometry : angle 0.50220 (32145) hydrogen bonds : bond 0.04358 ( 1435) hydrogen bonds : angle 3.49344 ( 4317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 0.993 Fit side-chains REVERT: A 359 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7118 (t80) REVERT: A 399 MET cc_start: 0.9088 (ttm) cc_final: 0.8836 (mtt) REVERT: A 459 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: A 544 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5972 (mtmt) REVERT: C 989 MET cc_start: 0.9021 (tpp) cc_final: 0.8693 (tpt) REVERT: C 994 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 66 outliers final: 56 residues processed: 163 average time/residue: 0.1391 time to fit residues: 39.9123 Evaluate side-chains 160 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 100 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 140 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 281 optimal weight: 0.0370 chunk 172 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 277 optimal weight: 7.9990 chunk 204 optimal weight: 0.0770 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.065524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.054399 restraints weight = 67687.418| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.94 r_work: 0.2784 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23569 Z= 0.093 Angle : 0.484 8.652 32145 Z= 0.242 Chirality : 0.039 0.137 3942 Planarity : 0.004 0.052 4070 Dihedral : 4.333 58.357 3657 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.72 % Allowed : 27.79 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.16), residues: 3054 helix: 2.48 (0.13), residues: 1662 sheet: 0.83 (0.25), residues: 441 loop : -0.68 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 978 TYR 0.011 0.001 TYR B 467 PHE 0.016 0.001 PHE B 397 TRP 0.006 0.001 TRP C 363 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00195 (23569) covalent geometry : angle 0.48406 (32145) hydrogen bonds : bond 0.03374 ( 1435) hydrogen bonds : angle 3.38429 ( 4317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.993 Fit side-chains REVERT: A 359 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 399 MET cc_start: 0.9021 (ttm) cc_final: 0.8806 (mtt) REVERT: A 544 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5672 (mtmt) REVERT: A 989 MET cc_start: 0.8833 (tpp) cc_final: 0.8459 (tpt) REVERT: B 721 MET cc_start: 0.8422 (mmm) cc_final: 0.8078 (mmm) REVERT: C 721 MET cc_start: 0.8798 (mmm) cc_final: 0.8442 (mmm) REVERT: C 827 TYR cc_start: 0.8593 (m-80) cc_final: 0.8300 (m-80) REVERT: C 989 MET cc_start: 0.8929 (tpp) cc_final: 0.8550 (tpt) REVERT: C 994 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8533 (mp) outliers start: 41 outliers final: 36 residues processed: 147 average time/residue: 0.1351 time to fit residues: 34.8925 Evaluate side-chains 143 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 958 LEU Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 141 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 187 optimal weight: 2.9990 chunk 216 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.052993 restraints weight = 68277.611| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.75 r_work: 0.2756 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23569 Z= 0.113 Angle : 0.494 8.798 32145 Z= 0.248 Chirality : 0.040 0.151 3942 Planarity : 0.004 0.051 4070 Dihedral : 4.316 57.811 3657 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.97 % Allowed : 27.75 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.16), residues: 3054 helix: 2.52 (0.13), residues: 1665 sheet: 0.85 (0.25), residues: 465 loop : -0.69 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.010 0.001 TYR B 467 PHE 0.016 0.001 PHE B 397 TRP 0.006 0.001 TRP C 190 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00262 (23569) covalent geometry : angle 0.49374 (32145) hydrogen bonds : bond 0.04101 ( 1435) hydrogen bonds : angle 3.42098 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.58 seconds wall clock time: 72 minutes 36.76 seconds (4356.76 seconds total)