Starting phenix.real_space_refine on Fri Jun 27 00:20:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653.map" model { file = "/net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atm_15653/06_2025/8atm_15653_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.020 sd= 0.841 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 227 5.16 5 C 19771 2.51 5 N 5239 2.21 5 O 5648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30885 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 15729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2035, 15729 Classifications: {'peptide': 2035} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 94, 'TRANS': 1939} Chain breaks: 31 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 15156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1963, 15156 Classifications: {'peptide': 1963} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 93, 'TRANS': 1868} Chain breaks: 30 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 18.90, per 1000 atoms: 0.61 Number of scatterers: 30885 At special positions: 0 Unit cell: (172.86, 206.4, 135.88, 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 227 16.00 O 5648 8.00 N 5239 7.00 C 19771 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: 7.96 Conformation dependent library (CDL) restraints added in 4.1 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7622 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 9 sheets defined 62.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 1313 through 1324 Processing helix chain 'A' and resid 1325 through 1337 removed outlier: 3.645A pdb=" N GLU A1329 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1364 Processing helix chain 'A' and resid 1378 through 1382 Processing helix chain 'A' and resid 1384 through 1393 Processing helix chain 'A' and resid 1397 through 1413 removed outlier: 3.988A pdb=" N SER A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1436 Processing helix chain 'A' and resid 1437 through 1442 Proline residue: A1440 - end of helix No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1444 through 1459 removed outlier: 3.589A pdb=" N VAL A1448 " --> pdb=" O THR A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1483 removed outlier: 3.648A pdb=" N ARG A1479 " --> pdb=" O THR A1475 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP A1483 " --> pdb=" O ARG A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1496 removed outlier: 4.038A pdb=" N ALA A1490 " --> pdb=" O THR A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1940 removed outlier: 3.678A pdb=" N ALA A1915 " --> pdb=" O ASP A1911 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A1919 " --> pdb=" O ALA A1915 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A1923 " --> pdb=" O ALA A1919 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS A1926 " --> pdb=" O GLU A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1960 through 1999 removed outlier: 3.704A pdb=" N LEU A1998 " --> pdb=" O LEU A1994 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A1999 " --> pdb=" O LYS A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2040 Processing helix chain 'A' and resid 2048 through 2054 removed outlier: 4.010A pdb=" N SER A2052 " --> pdb=" O ALA A2048 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A2053 " --> pdb=" O VAL A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2058 through 2067 Processing helix chain 'A' and resid 2071 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2113 through 2128 removed outlier: 3.594A pdb=" N ARG A2127 " --> pdb=" O CYS A2123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A2128 " --> pdb=" O ILE A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2164 through 2183 Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.344A pdb=" N SER A2330 " --> pdb=" O GLU A2326 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A2331 " --> pdb=" O ARG A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2365 removed outlier: 3.719A pdb=" N LEU A2351 " --> pdb=" O HIS A2347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A2356 " --> pdb=" O LEU A2352 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A2365 " --> pdb=" O ILE A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2375 removed outlier: 3.771A pdb=" N ILE A2374 " --> pdb=" O HIS A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2389 removed outlier: 3.820A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2420 Processing helix chain 'A' and resid 2575 through 2600 removed outlier: 3.872A pdb=" N ALA A2579 " --> pdb=" O LEU A2575 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A2581 " --> pdb=" O GLN A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2635 through 2649 Processing helix chain 'A' and resid 2656 through 2669 Processing helix chain 'A' and resid 2697 through 2711 removed outlier: 3.797A pdb=" N TRP A2710 " --> pdb=" O THR A2706 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2732 removed outlier: 3.850A pdb=" N ASN A2731 " --> pdb=" O THR A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2747 through 2754 Processing helix chain 'A' and resid 2755 through 2768 removed outlier: 4.384A pdb=" N ILE A2759 " --> pdb=" O ASP A2755 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS A2760 " --> pdb=" O PRO A2756 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2802 removed outlier: 3.740A pdb=" N THR A2786 " --> pdb=" O GLY A2782 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A2787 " --> pdb=" O PRO A2783 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A2802 " --> pdb=" O VAL A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2804 through 2821 removed outlier: 3.976A pdb=" N PHE A2808 " --> pdb=" O CYS A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 Processing helix chain 'A' and resid 2832 through 2844 Processing helix chain 'A' and resid 2853 through 2873 Processing helix chain 'A' and resid 2914 through 2930 removed outlier: 3.581A pdb=" N LEU A2918 " --> pdb=" O THR A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2986 removed outlier: 3.884A pdb=" N LEU A2983 " --> pdb=" O TYR A2979 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3000 Processing helix chain 'A' and resid 3005 through 3009 Processing helix chain 'A' and resid 3031 through 3046 Processing helix chain 'A' and resid 3049 through 3062 removed outlier: 3.547A pdb=" N MET A3053 " --> pdb=" O THR A3049 " (cutoff:3.500A) Proline residue: A3056 - end of helix Processing helix chain 'A' and resid 3064 through 3068 removed outlier: 3.650A pdb=" N GLY A3067 " --> pdb=" O GLY A3064 " (cutoff:3.500A) Processing helix chain 'A' and resid 3078 through 3089 Processing helix chain 'A' and resid 3091 through 3101 Processing helix chain 'A' and resid 3102 through 3117 removed outlier: 3.509A pdb=" N LEU A3106 " --> pdb=" O GLY A3102 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A3116 " --> pdb=" O VAL A3112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A3117 " --> pdb=" O THR A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3133 Processing helix chain 'A' and resid 3164 through 3167 Processing helix chain 'A' and resid 3179 through 3184 removed outlier: 3.649A pdb=" N LEU A3183 " --> pdb=" O GLU A3180 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3235 removed outlier: 3.623A pdb=" N THR A3234 " --> pdb=" O SER A3231 " (cutoff:3.500A) Processing helix chain 'A' and resid 3328 through 3340 Processing helix chain 'A' and resid 3344 through 3353 Processing helix chain 'A' and resid 3357 through 3367 Processing helix chain 'A' and resid 3374 through 3387 removed outlier: 3.728A pdb=" N ILE A3378 " --> pdb=" O HIS A3374 " (cutoff:3.500A) Processing helix chain 'A' and resid 3390 through 3402 Processing helix chain 'A' and resid 3428 through 3440 Processing helix chain 'A' and resid 3445 through 3464 Processing helix chain 'A' and resid 3490 through 3507 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.845A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3531 removed outlier: 3.627A pdb=" N PHE A3522 " --> pdb=" O ASP A3518 " (cutoff:3.500A) Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3565 removed outlier: 3.947A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A3558 " --> pdb=" O PRO A3554 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3617 Processing helix chain 'A' and resid 3621 through 3628 removed outlier: 3.952A pdb=" N GLN A3625 " --> pdb=" O GLU A3621 " (cutoff:3.500A) Processing helix chain 'A' and resid 3631 through 3645 removed outlier: 4.099A pdb=" N LEU A3635 " --> pdb=" O LEU A3631 " (cutoff:3.500A) Processing helix chain 'A' and resid 3682 through 3694 removed outlier: 3.626A pdb=" N ILE A3686 " --> pdb=" O LEU A3682 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3704 removed outlier: 3.746A pdb=" N GLY A3704 " --> pdb=" O LYS A3700 " (cutoff:3.500A) Processing helix chain 'A' and resid 3708 through 3720 removed outlier: 4.052A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A3713 " --> pdb=" O ASN A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 Processing helix chain 'A' and resid 3774 through 3791 removed outlier: 3.848A pdb=" N LYS A3779 " --> pdb=" O PRO A3775 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A3780 " --> pdb=" O ASN A3776 " (cutoff:3.500A) Processing helix chain 'A' and resid 3806 through 3816 Processing helix chain 'A' and resid 3846 through 3850 Processing helix chain 'A' and resid 3865 through 3874 Processing helix chain 'A' and resid 3982 through 3993 Processing helix chain 'A' and resid 4069 through 4077 removed outlier: 3.997A pdb=" N MET A4077 " --> pdb=" O VAL A4073 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4087 Processing helix chain 'A' and resid 4154 through 4165 Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.713A pdb=" N VAL A4173 " --> pdb=" O GLY A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4177 through 4189 Processing helix chain 'A' and resid 4199 through 4203 Processing helix chain 'A' and resid 4211 through 4224 Processing helix chain 'A' and resid 4228 through 4242 removed outlier: 3.847A pdb=" N VAL A4232 " --> pdb=" O THR A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4242 through 4256 Processing helix chain 'A' and resid 4306 through 4332 Processing helix chain 'A' and resid 4368 through 4379 removed outlier: 4.336A pdb=" N ASN A4379 " --> pdb=" O SER A4375 " (cutoff:3.500A) Processing helix chain 'A' and resid 4388 through 4405 removed outlier: 3.547A pdb=" N CYS A4405 " --> pdb=" O ALA A4401 " (cutoff:3.500A) Processing helix chain 'A' and resid 4406 through 4412 Proline residue: A4410 - end of helix Processing helix chain 'A' and resid 4432 through 4451 Processing helix chain 'A' and resid 4483 through 4501 removed outlier: 3.722A pdb=" N GLU A4501 " --> pdb=" O GLN A4497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1394 Processing helix chain 'B' and resid 1397 through 1413 removed outlier: 3.685A pdb=" N ALA B1401 " --> pdb=" O GLY B1397 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1413 " --> pdb=" O ALA B1409 " (cutoff:3.500A) Processing helix chain 'B' and resid 1424 through 1437 removed outlier: 4.214A pdb=" N SER B1437 " --> pdb=" O LEU B1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1442 Processing helix chain 'B' and resid 1444 through 1447 Processing helix chain 'B' and resid 1448 through 1459 Processing helix chain 'B' and resid 1460 through 1462 No H-bonds generated for 'chain 'B' and resid 1460 through 1462' Processing helix chain 'B' and resid 1464 through 1483 removed outlier: 3.885A pdb=" N ARG B1479 " --> pdb=" O THR B1475 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B1480 " --> pdb=" O ALA B1476 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B1483 " --> pdb=" O ARG B1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1496 Processing helix chain 'B' and resid 1912 through 1940 removed outlier: 3.843A pdb=" N VAL B1918 " --> pdb=" O LEU B1914 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B1919 " --> pdb=" O ALA B1915 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B1920 " --> pdb=" O MET B1916 " (cutoff:3.500A) Processing helix chain 'B' and resid 1949 through 1958 Processing helix chain 'B' and resid 1960 through 1998 removed outlier: 3.701A pdb=" N VAL B1964 " --> pdb=" O PRO B1960 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B1965 " --> pdb=" O ASP B1961 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B1966 " --> pdb=" O LYS B1962 " (cutoff:3.500A) Processing helix chain 'B' and resid 2014 through 2018 Processing helix chain 'B' and resid 2019 through 2041 Processing helix chain 'B' and resid 2048 through 2054 Processing helix chain 'B' and resid 2058 through 2067 Processing helix chain 'B' and resid 2071 through 2086 Processing helix chain 'B' and resid 2093 through 2104 Processing helix chain 'B' and resid 2113 through 2129 Processing helix chain 'B' and resid 2132 through 2146 removed outlier: 3.807A pdb=" N GLU B2136 " --> pdb=" O SER B2132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2164 through 2183 Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.825A pdb=" N CYS B2328 " --> pdb=" O ALA B2324 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B2329 " --> pdb=" O HIS B2325 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER B2330 " --> pdb=" O GLU B2326 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B2331 " --> pdb=" O ARG B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2365 removed outlier: 3.689A pdb=" N LEU B2351 " --> pdb=" O HIS B2347 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B2353 " --> pdb=" O ASP B2349 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B2356 " --> pdb=" O LEU B2352 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B2365 " --> pdb=" O ILE B2361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2370 through 2375 removed outlier: 3.536A pdb=" N ILE B2374 " --> pdb=" O HIS B2370 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2389 removed outlier: 3.776A pdb=" N LEU B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2400 through 2420 removed outlier: 4.039A pdb=" N ALA B2404 " --> pdb=" O GLY B2400 " (cutoff:3.500A) Processing helix chain 'B' and resid 2576 through 2600 removed outlier: 4.152A pdb=" N MET B2582 " --> pdb=" O GLN B2578 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2649 Processing helix chain 'B' and resid 2656 through 2669 Processing helix chain 'B' and resid 2697 through 2711 removed outlier: 3.787A pdb=" N TRP B2710 " --> pdb=" O THR B2706 " (cutoff:3.500A) Processing helix chain 'B' and resid 2715 through 2732 removed outlier: 3.842A pdb=" N ASN B2731 " --> pdb=" O THR B2727 " (cutoff:3.500A) Processing helix chain 'B' and resid 2747 through 2754 Processing helix chain 'B' and resid 2755 through 2768 removed outlier: 4.400A pdb=" N ILE B2759 " --> pdb=" O ASP B2755 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B2760 " --> pdb=" O PRO B2756 " (cutoff:3.500A) Processing helix chain 'B' and resid 2782 through 2802 removed outlier: 3.756A pdb=" N THR B2786 " --> pdb=" O GLY B2782 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B2787 " --> pdb=" O PRO B2783 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER B2802 " --> pdb=" O VAL B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2804 through 2821 removed outlier: 4.056A pdb=" N PHE B2808 " --> pdb=" O CYS B2804 " (cutoff:3.500A) Processing helix chain 'B' and resid 2824 through 2829 Processing helix chain 'B' and resid 2832 through 2844 Processing helix chain 'B' and resid 2853 through 2873 Processing helix chain 'B' and resid 2914 through 2930 removed outlier: 3.521A pdb=" N LEU B2918 " --> pdb=" O THR B2914 " (cutoff:3.500A) Processing helix chain 'B' and resid 2979 through 2986 removed outlier: 3.875A pdb=" N LEU B2983 " --> pdb=" O TYR B2979 " (cutoff:3.500A) Processing helix chain 'B' and resid 2987 through 3000 removed outlier: 3.539A pdb=" N LEU B3000 " --> pdb=" O SER B2996 " (cutoff:3.500A) Processing helix chain 'B' and resid 3004 through 3008 removed outlier: 3.571A pdb=" N MET B3008 " --> pdb=" O ALA B3005 " (cutoff:3.500A) Processing helix chain 'B' and resid 3031 through 3046 Processing helix chain 'B' and resid 3049 through 3062 removed outlier: 3.599A pdb=" N MET B3053 " --> pdb=" O THR B3049 " (cutoff:3.500A) Proline residue: B3056 - end of helix Processing helix chain 'B' and resid 3064 through 3068 removed outlier: 3.721A pdb=" N GLY B3067 " --> pdb=" O GLY B3064 " (cutoff:3.500A) Processing helix chain 'B' and resid 3078 through 3089 Processing helix chain 'B' and resid 3091 through 3101 Processing helix chain 'B' and resid 3102 through 3117 removed outlier: 3.761A pdb=" N ARG B3116 " --> pdb=" O VAL B3112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B3117 " --> pdb=" O THR B3113 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3131 removed outlier: 3.503A pdb=" N THR B3128 " --> pdb=" O SER B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3164 through 3167 Processing helix chain 'B' and resid 3179 through 3184 removed outlier: 3.626A pdb=" N LEU B3183 " --> pdb=" O GLU B3180 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B3184 " --> pdb=" O VAL B3181 " (cutoff:3.500A) Processing helix chain 'B' and resid 3231 through 3235 removed outlier: 3.641A pdb=" N THR B3234 " --> pdb=" O SER B3231 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3326 Processing helix chain 'B' and resid 3327 through 3340 removed outlier: 4.325A pdb=" N LEU B3331 " --> pdb=" O SER B3327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3341 through 3343 No H-bonds generated for 'chain 'B' and resid 3341 through 3343' Processing helix chain 'B' and resid 3344 through 3353 Processing helix chain 'B' and resid 3357 through 3367 Processing helix chain 'B' and resid 3374 through 3387 removed outlier: 3.795A pdb=" N ILE B3378 " --> pdb=" O HIS B3374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3390 through 3402 Processing helix chain 'B' and resid 3428 through 3441 Processing helix chain 'B' and resid 3445 through 3465 removed outlier: 3.807A pdb=" N ARG B3449 " --> pdb=" O GLY B3445 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B3450 " --> pdb=" O THR B3446 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B3465 " --> pdb=" O ALA B3461 " (cutoff:3.500A) Processing helix chain 'B' and resid 3490 through 3507 Processing helix chain 'B' and resid 3512 through 3517 removed outlier: 3.800A pdb=" N LEU B3516 " --> pdb=" O ASP B3512 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B3517 " --> pdb=" O LEU B3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3512 through 3517' Processing helix chain 'B' and resid 3518 through 3532 removed outlier: 3.654A pdb=" N PHE B3522 " --> pdb=" O ASP B3518 " (cutoff:3.500A) Processing helix chain 'B' and resid 3536 through 3553 Processing helix chain 'B' and resid 3553 through 3564 removed outlier: 3.986A pdb=" N PHE B3557 " --> pdb=" O HIS B3553 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B3558 " --> pdb=" O PRO B3554 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3617 Processing helix chain 'B' and resid 3619 through 3628 removed outlier: 4.102A pdb=" N LYS B3624 " --> pdb=" O PRO B3620 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B3625 " --> pdb=" O GLU B3621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3631 through 3645 removed outlier: 3.904A pdb=" N LEU B3635 " --> pdb=" O LEU B3631 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B3640 " --> pdb=" O VAL B3636 " (cutoff:3.500A) Processing helix chain 'B' and resid 3682 through 3694 removed outlier: 3.587A pdb=" N ILE B3686 " --> pdb=" O LEU B3682 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3704 Processing helix chain 'B' and resid 3708 through 3720 removed outlier: 4.224A pdb=" N TRP B3712 " --> pdb=" O VAL B3708 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B3713 " --> pdb=" O ASN B3709 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 Processing helix chain 'B' and resid 3774 through 3791 removed outlier: 3.518A pdb=" N GLN B3778 " --> pdb=" O HIS B3774 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B3779 " --> pdb=" O PRO B3775 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B3780 " --> pdb=" O ASN B3776 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B3791 " --> pdb=" O GLU B3787 " (cutoff:3.500A) Processing helix chain 'B' and resid 3806 through 3816 Processing helix chain 'B' and resid 3846 through 3850 Processing helix chain 'B' and resid 3865 through 3874 Processing helix chain 'B' and resid 3982 through 3993 Processing helix chain 'B' and resid 4069 through 4077 removed outlier: 3.645A pdb=" N MET B4077 " --> pdb=" O VAL B4073 " (cutoff:3.500A) Processing helix chain 'B' and resid 4078 through 4086 removed outlier: 4.196A pdb=" N LEU B4082 " --> pdb=" O GLY B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4165 removed outlier: 3.584A pdb=" N LEU B4158 " --> pdb=" O PRO B4154 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 removed outlier: 3.614A pdb=" N VAL B4173 " --> pdb=" O GLY B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4177 through 4189 Processing helix chain 'B' and resid 4199 through 4203 Processing helix chain 'B' and resid 4211 through 4224 Processing helix chain 'B' and resid 4228 through 4241 removed outlier: 4.014A pdb=" N VAL B4232 " --> pdb=" O THR B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4242 through 4255 Processing helix chain 'B' and resid 4306 through 4332 Processing helix chain 'B' and resid 4368 through 4378 Processing helix chain 'B' and resid 4388 through 4405 removed outlier: 3.531A pdb=" N TYR B4392 " --> pdb=" O HIS B4388 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B4405 " --> pdb=" O ALA B4401 " (cutoff:3.500A) Processing helix chain 'B' and resid 4408 through 4412 Processing helix chain 'B' and resid 4432 through 4451 Processing helix chain 'B' and resid 4483 through 4501 removed outlier: 3.792A pdb=" N GLU B4501 " --> pdb=" O GLN B4497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1511 through 1512 Processing sheet with id=AA2, first strand: chain 'A' and resid 1521 through 1522 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1521 through 1522 current: chain 'A' and resid 1789 through 1806 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1789 through 1806 current: chain 'A' and resid 1829 through 1834 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1777 through 1779 Processing sheet with id=AA4, first strand: chain 'A' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2877 through 2879 current: chain 'A' and resid 3251 through 3252 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 2891 through 2892 Processing sheet with id=AA6, first strand: chain 'A' and resid 3855 through 3861 Processing sheet with id=AA7, first strand: chain 'B' and resid 1789 through 1805 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1789 through 1805 current: chain 'B' and resid 1829 through 1834 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 2877 through 2879 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2877 through 2879 current: chain 'B' and resid 3251 through 3252 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 3855 through 3861 removed outlier: 9.611A pdb=" N ILE B4002 " --> pdb=" O LYS B3821 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B3823 " --> pdb=" O ILE B4002 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B4004 " --> pdb=" O THR B3823 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE B3825 " --> pdb=" O LEU B4004 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B4006 " --> pdb=" O PHE B3825 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN B3827 " --> pdb=" O VAL B4006 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU B4008 " --> pdb=" O GLN B3827 " (cutoff:3.500A) 1651 hydrogen bonds defined for protein. 4851 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: 12.22 Time building geometry restraints manager: 9.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9912 1.34 - 1.46: 5176 1.46 - 1.58: 16008 1.58 - 1.70: 0 1.70 - 1.82: 345 Bond restraints: 31441 Sorted by residual: bond pdb=" N SER B1478 " pdb=" CA SER B1478 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.26e+00 bond pdb=" N ARG B1479 " pdb=" CA ARG B1479 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.32e+00 bond pdb=" N GLN B1482 " pdb=" CA GLN B1482 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.25e-02 6.40e+03 3.95e+00 bond pdb=" CA SER B1478 " pdb=" CB SER B1478 " ideal model delta sigma weight residual 1.530 1.500 0.030 1.56e-02 4.11e+03 3.65e+00 bond pdb=" N LEU B1481 " pdb=" CA LEU B1481 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.52e+00 ... (remaining 31436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 42003 1.88 - 3.77: 580 3.77 - 5.65: 106 5.65 - 7.54: 14 7.54 - 9.42: 3 Bond angle restraints: 42706 Sorted by residual: angle pdb=" N GLY A2574 " pdb=" CA GLY A2574 " pdb=" C GLY A2574 " ideal model delta sigma weight residual 112.77 117.31 -4.54 1.28e+00 6.10e-01 1.26e+01 angle pdb=" N GLU B4318 " pdb=" CA GLU B4318 " pdb=" CB GLU B4318 " ideal model delta sigma weight residual 110.28 114.80 -4.52 1.55e+00 4.16e-01 8.50e+00 angle pdb=" N GLN A1992 " pdb=" CA GLN A1992 " pdb=" CB GLN A1992 " ideal model delta sigma weight residual 110.28 114.78 -4.50 1.55e+00 4.16e-01 8.43e+00 angle pdb=" C ALA B3047 " pdb=" N SER B3048 " pdb=" CA SER B3048 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.21e+00 angle pdb=" N GLN B1480 " pdb=" CA GLN B1480 " pdb=" C GLN B1480 " ideal model delta sigma weight residual 111.28 108.20 3.08 1.09e+00 8.42e-01 7.98e+00 ... (remaining 42701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17242 17.94 - 35.88: 1495 35.88 - 53.82: 237 53.82 - 71.76: 54 71.76 - 89.70: 25 Dihedral angle restraints: 19053 sinusoidal: 7414 harmonic: 11639 Sorted by residual: dihedral pdb=" CA MET B1916 " pdb=" C MET B1916 " pdb=" N MET B1917 " pdb=" CA MET B1917 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PRO A3632 " pdb=" C PRO A3632 " pdb=" N SER A3633 " pdb=" CA SER A3633 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A3999 " pdb=" C TYR A3999 " pdb=" N ARG A4000 " pdb=" CA ARG A4000 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 19050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4177 0.046 - 0.092: 837 0.092 - 0.139: 193 0.139 - 0.185: 17 0.185 - 0.231: 2 Chirality restraints: 5226 Sorted by residual: chirality pdb=" CA GLN A1992 " pdb=" N GLN A1992 " pdb=" C GLN A1992 " pdb=" CB GLN A1992 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE A1817 " pdb=" N ILE A1817 " pdb=" C ILE A1817 " pdb=" CB ILE A1817 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU B1481 " pdb=" N LEU B1481 " pdb=" C LEU B1481 " pdb=" CB LEU B1481 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 5223 not shown) Planarity restraints: 5319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B1477 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C VAL B1477 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL B1477 " 0.016 2.00e-02 2.50e+03 pdb=" N SER B1478 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B3846 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B3847 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B3847 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B3847 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2071 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A2072 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A2072 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2072 " -0.028 5.00e-02 4.00e+02 ... (remaining 5316 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2560 2.74 - 3.28: 31127 3.28 - 3.82: 49681 3.82 - 4.36: 55277 4.36 - 4.90: 97383 Nonbonded interactions: 236028 Sorted by model distance: nonbonded pdb=" OH TYR B2104 " pdb=" O GLN B2114 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR B3302 " pdb=" OG1 THR B3307 " model vdw 2.215 3.040 nonbonded pdb=" O ARG B3688 " pdb=" OG1 THR B3691 " model vdw 2.224 3.040 nonbonded pdb=" O ILE B1806 " pdb=" OG SER B1841 " model vdw 2.233 3.040 nonbonded pdb=" O ASP A2013 " pdb=" OG1 THR A2017 " model vdw 2.243 3.040 ... (remaining 236023 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 1384 through 1525 or resid 1770 through 1781 or resid 1785 \ through 3131 or resid 3160 through 3308 or resid 3321 through 4502)) selection = (chain 'B' and (resid 1384 through 1864 or resid 1871 through 2004 or resid 2011 \ through 2325 or (resid 2326 and (name N or name CA or name C or name O or name \ CB )) or resid 2327 through 4502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 71.490 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 0.041 31441 Z= 0.155 Angle : 0.566 9.424 42706 Z= 0.290 Chirality : 0.039 0.231 5226 Planarity : 0.004 0.055 5319 Dihedral : 14.027 89.699 11431 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.06 % Allowed : 0.11 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.14), residues: 3872 helix: 2.38 (0.11), residues: 2215 sheet: 1.47 (0.34), residues: 244 loop : -0.79 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3702 HIS 0.010 0.001 HIS B2654 PHE 0.016 0.001 PHE A1384 TYR 0.019 0.001 TYR A1521 ARG 0.005 0.000 ARG A2915 Details of bonding type rmsd hydrogen bonds : bond 0.13837 ( 1651) hydrogen bonds : angle 4.79960 ( 4851) covalent geometry : bond 0.00358 (31441) covalent geometry : angle 0.56628 (42706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 3.100 Fit side-chains revert: symmetry clash REVERT: A 1473 LEU cc_start: 0.9317 (tp) cc_final: 0.9114 (tp) REVERT: A 3771 ILE cc_start: 0.8218 (tp) cc_final: 0.8006 (tp) REVERT: A 3816 MET cc_start: 0.7723 (mmt) cc_final: 0.7457 (mmt) REVERT: A 4373 MET cc_start: 0.7862 (mtm) cc_final: 0.7631 (mtm) REVERT: B 1492 LEU cc_start: 0.9270 (tp) cc_final: 0.9066 (tp) REVERT: B 2582 MET cc_start: 0.8087 (tpp) cc_final: 0.7840 (ttp) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 0.3645 time to fit residues: 139.4922 Evaluate side-chains 197 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1478 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 1.9990 chunk 302 optimal weight: 0.0050 chunk 167 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 312 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3442 GLN A3493 HIS A3859 HIS A4180 HIS A4182 GLN A4366 GLN B1480 GLN B1929 ASN ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071921 restraints weight = 85007.489| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.34 r_work: 0.2778 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31441 Z= 0.107 Angle : 0.518 11.972 42706 Z= 0.259 Chirality : 0.037 0.187 5226 Planarity : 0.004 0.052 5319 Dihedral : 3.670 21.952 4188 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.29 % Allowed : 5.20 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.14), residues: 3872 helix: 2.56 (0.11), residues: 2261 sheet: 1.58 (0.34), residues: 247 loop : -0.75 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B1820 HIS 0.008 0.001 HIS B2654 PHE 0.021 0.001 PHE B3807 TYR 0.016 0.001 TYR A3505 ARG 0.007 0.000 ARG A4236 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1651) hydrogen bonds : angle 3.68932 ( 4851) covalent geometry : bond 0.00224 (31441) covalent geometry : angle 0.51790 (42706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 3.461 Fit side-chains REVERT: A 3699 MET cc_start: 0.8667 (tpp) cc_final: 0.8441 (tpp) REVERT: A 4077 MET cc_start: 0.7392 (ppp) cc_final: 0.7177 (ppp) REVERT: B 1492 LEU cc_start: 0.9188 (tp) cc_final: 0.8985 (tp) REVERT: B 2582 MET cc_start: 0.8054 (tpp) cc_final: 0.7844 (ttp) REVERT: B 2878 MET cc_start: 0.8559 (tpt) cc_final: 0.8356 (tpt) REVERT: B 3718 LEU cc_start: 0.8702 (tt) cc_final: 0.8307 (mt) REVERT: B 3975 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8636 (tp-100) REVERT: B 4077 MET cc_start: 0.8836 (mmp) cc_final: 0.8552 (mmm) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.3672 time to fit residues: 132.7416 Evaluate side-chains 202 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1916 MET Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2038 LEU Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3873 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 258 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 189 optimal weight: 50.0000 chunk 234 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1989 ASN A4180 HIS ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1456 ASN ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.115379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.067535 restraints weight = 84960.304| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.85 r_work: 0.2726 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31441 Z= 0.216 Angle : 0.568 12.634 42706 Z= 0.283 Chirality : 0.040 0.154 5226 Planarity : 0.004 0.054 5319 Dihedral : 3.794 21.723 4187 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.71 % Allowed : 8.00 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3872 helix: 2.53 (0.11), residues: 2257 sheet: 1.48 (0.34), residues: 240 loop : -0.89 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1820 HIS 0.009 0.001 HIS B2654 PHE 0.017 0.001 PHE B2811 TYR 0.016 0.001 TYR A1521 ARG 0.005 0.000 ARG A2915 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 1651) hydrogen bonds : angle 3.74480 ( 4851) covalent geometry : bond 0.00524 (31441) covalent geometry : angle 0.56778 (42706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 3.261 Fit side-chains revert: symmetry clash REVERT: A 3699 MET cc_start: 0.8657 (tpp) cc_final: 0.8343 (tpp) REVERT: A 3709 ASN cc_start: 0.9099 (m110) cc_final: 0.8656 (m110) REVERT: B 1455 LEU cc_start: 0.8390 (mm) cc_final: 0.8162 (mm) REVERT: B 1875 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5323 (pp) REVERT: B 1917 MET cc_start: 0.7852 (mmp) cc_final: 0.7507 (mmp) REVERT: B 2582 MET cc_start: 0.8088 (tpp) cc_final: 0.7787 (ttp) REVERT: B 3718 LEU cc_start: 0.8723 (tt) cc_final: 0.8315 (mt) REVERT: B 3981 MET cc_start: 0.8129 (ptm) cc_final: 0.7845 (ptm) outliers start: 25 outliers final: 12 residues processed: 226 average time/residue: 0.3716 time to fit residues: 145.8160 Evaluate side-chains 212 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 3347 MET Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4215 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2059 CYS Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain B residue 4211 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 279 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 chunk 317 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069786 restraints weight = 84603.106| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.22 r_work: 0.2733 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31441 Z= 0.129 Angle : 0.516 13.882 42706 Z= 0.254 Chirality : 0.037 0.211 5226 Planarity : 0.004 0.053 5319 Dihedral : 3.673 22.146 4187 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.94 % Allowed : 9.60 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.14), residues: 3872 helix: 2.62 (0.11), residues: 2259 sheet: 1.54 (0.34), residues: 238 loop : -0.87 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1820 HIS 0.007 0.001 HIS B2654 PHE 0.014 0.001 PHE B3807 TYR 0.014 0.001 TYR A1521 ARG 0.003 0.000 ARG A2915 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1651) hydrogen bonds : angle 3.57335 ( 4851) covalent geometry : bond 0.00304 (31441) covalent geometry : angle 0.51613 (42706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 2.963 Fit side-chains REVERT: A 3699 MET cc_start: 0.8532 (tpp) cc_final: 0.8224 (tpp) REVERT: A 3709 ASN cc_start: 0.9082 (m110) cc_final: 0.8671 (m110) REVERT: A 3816 MET cc_start: 0.7724 (mmt) cc_final: 0.7512 (mmt) REVERT: B 1455 LEU cc_start: 0.8371 (mm) cc_final: 0.8136 (mm) REVERT: B 1875 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5372 (pp) REVERT: B 1917 MET cc_start: 0.7801 (mmp) cc_final: 0.7406 (mmp) REVERT: B 3718 LEU cc_start: 0.8688 (tt) cc_final: 0.8288 (mt) REVERT: B 3975 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8627 (tp-100) REVERT: B 3981 MET cc_start: 0.8063 (ptm) cc_final: 0.7497 (ptm) REVERT: B 4077 MET cc_start: 0.8701 (mmp) cc_final: 0.8395 (mmm) outliers start: 33 outliers final: 15 residues processed: 228 average time/residue: 0.3605 time to fit residues: 143.4350 Evaluate side-chains 217 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3347 MET Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4215 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4211 THR Chi-restraints excluded: chain B residue 4215 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 115 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 337 optimal weight: 0.9980 chunk 331 optimal weight: 7.9990 chunk 385 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 224 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3109 ASN A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068578 restraints weight = 84374.128| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.85 r_work: 0.2749 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31441 Z= 0.142 Angle : 0.523 14.480 42706 Z= 0.256 Chirality : 0.038 0.178 5226 Planarity : 0.004 0.055 5319 Dihedral : 3.637 21.954 4187 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.74 % Allowed : 11.26 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3872 helix: 2.67 (0.11), residues: 2254 sheet: 1.65 (0.34), residues: 236 loop : -0.83 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1820 HIS 0.007 0.001 HIS B2654 PHE 0.013 0.001 PHE B3807 TYR 0.015 0.001 TYR A1521 ARG 0.003 0.000 ARG A2915 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 1651) hydrogen bonds : angle 3.53993 ( 4851) covalent geometry : bond 0.00339 (31441) covalent geometry : angle 0.52323 (42706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 3.476 Fit side-chains revert: symmetry clash REVERT: A 3699 MET cc_start: 0.8541 (tpp) cc_final: 0.8259 (tpp) REVERT: A 3709 ASN cc_start: 0.9112 (m110) cc_final: 0.8686 (m110) REVERT: A 3816 MET cc_start: 0.7862 (mmt) cc_final: 0.7656 (mmt) REVERT: B 1455 LEU cc_start: 0.8449 (mm) cc_final: 0.8194 (mm) REVERT: B 1875 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5366 (pp) REVERT: B 1917 MET cc_start: 0.7882 (mmp) cc_final: 0.7449 (mmp) REVERT: B 2582 MET cc_start: 0.8211 (tpp) cc_final: 0.7923 (ttp) REVERT: B 3975 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8633 (tp-100) outliers start: 26 outliers final: 18 residues processed: 227 average time/residue: 0.3660 time to fit residues: 143.9960 Evaluate side-chains 221 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1992 GLN Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3347 MET Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4215 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4211 THR Chi-restraints excluded: chain B residue 4215 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 52 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 259 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 222 optimal weight: 50.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1435 ASN A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.115662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068125 restraints weight = 84564.560| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.86 r_work: 0.2741 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31441 Z= 0.160 Angle : 0.539 14.804 42706 Z= 0.263 Chirality : 0.038 0.174 5226 Planarity : 0.004 0.053 5319 Dihedral : 3.670 21.874 4187 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.17 % Allowed : 11.77 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.14), residues: 3872 helix: 2.65 (0.11), residues: 2254 sheet: 1.47 (0.34), residues: 246 loop : -0.82 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1820 HIS 0.006 0.001 HIS B2654 PHE 0.023 0.001 PHE A3557 TYR 0.018 0.001 TYR B1457 ARG 0.004 0.000 ARG A2915 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 1651) hydrogen bonds : angle 3.58150 ( 4851) covalent geometry : bond 0.00385 (31441) covalent geometry : angle 0.53873 (42706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1353 LEU cc_start: 0.9004 (tp) cc_final: 0.8760 (pp) REVERT: A 2878 MET cc_start: 0.8381 (tpt) cc_final: 0.7914 (tpt) REVERT: A 3561 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: A 3607 GLU cc_start: 0.8833 (mp0) cc_final: 0.8580 (mt-10) REVERT: B 1455 LEU cc_start: 0.8482 (mm) cc_final: 0.8235 (mm) REVERT: B 1875 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5392 (pp) REVERT: B 1917 MET cc_start: 0.7902 (mmp) cc_final: 0.7457 (mmp) REVERT: B 2714 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8798 (p) REVERT: B 3101 MET cc_start: 0.9110 (mtt) cc_final: 0.8885 (mtt) REVERT: B 3848 MET cc_start: 0.9437 (ptp) cc_final: 0.9218 (ptp) REVERT: B 4077 MET cc_start: 0.8727 (mmp) cc_final: 0.8483 (mmm) outliers start: 41 outliers final: 26 residues processed: 237 average time/residue: 0.6220 time to fit residues: 261.4634 Evaluate side-chains 233 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 5.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1992 GLN Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2349 ASP Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3347 MET Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3561 MET Chi-restraints excluded: chain A residue 3639 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4187 LEU Chi-restraints excluded: chain A residue 4215 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2714 THR Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3385 ILE Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4211 THR Chi-restraints excluded: chain B residue 4215 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 75 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 217 optimal weight: 0.0060 chunk 15 optimal weight: 20.0000 chunk 54 optimal weight: 0.0970 chunk 128 optimal weight: 8.9990 chunk 303 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2775 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069208 restraints weight = 84301.761| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.88 r_work: 0.2767 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31441 Z= 0.110 Angle : 0.516 14.140 42706 Z= 0.249 Chirality : 0.037 0.178 5226 Planarity : 0.004 0.051 5319 Dihedral : 3.570 22.083 4187 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.94 % Allowed : 12.46 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3872 helix: 2.71 (0.11), residues: 2265 sheet: 1.62 (0.34), residues: 240 loop : -0.79 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1820 HIS 0.006 0.001 HIS B2654 PHE 0.018 0.001 PHE A3557 TYR 0.014 0.001 TYR A1521 ARG 0.002 0.000 ARG B4236 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1651) hydrogen bonds : angle 3.48012 ( 4851) covalent geometry : bond 0.00254 (31441) covalent geometry : angle 0.51578 (42706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 3.877 Fit side-chains REVERT: A 1353 LEU cc_start: 0.8982 (tp) cc_final: 0.8749 (pp) REVERT: A 1992 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: A 3561 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: A 3699 MET cc_start: 0.8657 (tpp) cc_final: 0.8290 (tpp) REVERT: B 1455 LEU cc_start: 0.8498 (mm) cc_final: 0.8254 (mm) REVERT: B 1875 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5386 (pp) REVERT: B 1917 MET cc_start: 0.7865 (mmp) cc_final: 0.7400 (mmp) REVERT: B 3101 MET cc_start: 0.9038 (mtt) cc_final: 0.8835 (mtt) REVERT: B 3848 MET cc_start: 0.9417 (ptp) cc_final: 0.9208 (ptp) REVERT: B 3975 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8608 (tp-100) REVERT: B 4077 MET cc_start: 0.8683 (mmp) cc_final: 0.8429 (mmm) outliers start: 33 outliers final: 20 residues processed: 229 average time/residue: 0.4008 time to fit residues: 158.9700 Evaluate side-chains 224 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1992 GLN Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3347 MET Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3561 MET Chi-restraints excluded: chain A residue 3639 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4215 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2772 HIS Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3385 ILE Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Chi-restraints excluded: chain B residue 3871 ASP Chi-restraints excluded: chain B residue 4187 LEU Chi-restraints excluded: chain B residue 4211 THR Chi-restraints excluded: chain B residue 4215 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 127 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 280 optimal weight: 0.0370 chunk 292 optimal weight: 6.9990 chunk 369 optimal weight: 0.0030 chunk 92 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 0.1980 chunk 278 optimal weight: 0.8980 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072349 restraints weight = 85558.819| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.27 r_work: 0.2804 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31441 Z= 0.089 Angle : 0.509 15.777 42706 Z= 0.243 Chirality : 0.036 0.275 5226 Planarity : 0.004 0.049 5319 Dihedral : 3.388 22.612 4187 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.46 % Allowed : 13.29 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3872 helix: 2.72 (0.11), residues: 2287 sheet: 1.81 (0.35), residues: 241 loop : -0.65 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B2710 HIS 0.005 0.001 HIS B2654 PHE 0.021 0.001 PHE B3807 TYR 0.013 0.001 TYR A1521 ARG 0.004 0.000 ARG A2823 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 1651) hydrogen bonds : angle 3.36449 ( 4851) covalent geometry : bond 0.00189 (31441) covalent geometry : angle 0.50903 (42706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 3.328 Fit side-chains REVERT: A 1856 MET cc_start: 0.8640 (tpt) cc_final: 0.8243 (tpp) REVERT: A 3561 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7948 (mtt) REVERT: A 3699 MET cc_start: 0.8605 (tpp) cc_final: 0.8237 (tpp) REVERT: A 4237 MET cc_start: 0.8338 (mmm) cc_final: 0.7630 (ttt) REVERT: A 4373 MET cc_start: 0.7589 (mtm) cc_final: 0.7374 (mtt) REVERT: B 1455 LEU cc_start: 0.8489 (mm) cc_final: 0.8256 (mm) REVERT: B 1875 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5381 (pp) REVERT: B 1917 MET cc_start: 0.7811 (mmp) cc_final: 0.7348 (mmp) REVERT: B 3718 LEU cc_start: 0.8701 (tt) cc_final: 0.8314 (mt) REVERT: B 3848 MET cc_start: 0.9425 (ptp) cc_final: 0.9187 (ptp) REVERT: B 3975 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8555 (tp-100) REVERT: B 4077 MET cc_start: 0.8562 (mmp) cc_final: 0.8297 (mmm) outliers start: 16 outliers final: 8 residues processed: 233 average time/residue: 0.3842 time to fit residues: 153.6225 Evaluate side-chains 217 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3561 MET Chi-restraints excluded: chain A residue 3639 LEU Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 2772 HIS Chi-restraints excluded: chain B residue 3488 MET Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Chi-restraints excluded: chain B residue 4187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 383 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 270 optimal weight: 0.5980 chunk 312 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1328 HIS ** A1988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068656 restraints weight = 84727.144| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.86 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: 0.8680 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31441 Z= 0.153 Angle : 0.550 15.591 42706 Z= 0.265 Chirality : 0.038 0.246 5226 Planarity : 0.004 0.050 5319 Dihedral : 3.506 26.996 4187 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.66 % Allowed : 13.43 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.14), residues: 3872 helix: 2.73 (0.11), residues: 2262 sheet: 1.87 (0.35), residues: 234 loop : -0.69 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B1820 HIS 0.019 0.001 HIS A1988 PHE 0.040 0.001 PHE B4164 TYR 0.019 0.001 TYR B1457 ARG 0.004 0.000 ARG A2823 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1651) hydrogen bonds : angle 3.49468 ( 4851) covalent geometry : bond 0.00366 (31441) covalent geometry : angle 0.54987 (42706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 3.896 Fit side-chains REVERT: A 1856 MET cc_start: 0.8598 (tpt) cc_final: 0.8154 (tpp) REVERT: A 3561 MET cc_start: 0.8328 (mtm) cc_final: 0.8076 (mtt) REVERT: A 3699 MET cc_start: 0.8668 (tpp) cc_final: 0.8287 (tpp) REVERT: A 3816 MET cc_start: 0.8020 (mmt) cc_final: 0.7805 (mmt) REVERT: A 4373 MET cc_start: 0.7598 (mtm) cc_final: 0.7377 (mtt) REVERT: B 1455 LEU cc_start: 0.8504 (mm) cc_final: 0.8255 (mm) REVERT: B 1875 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5376 (pp) REVERT: B 1917 MET cc_start: 0.7828 (mmp) cc_final: 0.7337 (mmp) REVERT: B 1994 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6939 (mp) REVERT: B 3549 MET cc_start: 0.8342 (tpp) cc_final: 0.8064 (mtp) REVERT: B 3848 MET cc_start: 0.9437 (ptp) cc_final: 0.9209 (ptp) REVERT: B 3975 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8569 (tp-100) outliers start: 23 outliers final: 16 residues processed: 226 average time/residue: 0.3501 time to fit residues: 138.2224 Evaluate side-chains 221 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3125 MET Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3639 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2134 VAL Chi-restraints excluded: chain B residue 2781 VAL Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3385 ILE Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Chi-restraints excluded: chain B residue 4187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 250 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 358 optimal weight: 0.9990 chunk 294 optimal weight: 0.3980 chunk 181 optimal weight: 40.0000 chunk 295 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 343 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.116701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069316 restraints weight = 84800.710| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.84 r_work: 0.2773 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31441 Z= 0.117 Angle : 0.538 15.573 42706 Z= 0.256 Chirality : 0.037 0.249 5226 Planarity : 0.004 0.050 5319 Dihedral : 3.483 24.485 4187 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.51 % Allowed : 13.69 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3872 helix: 2.74 (0.11), residues: 2265 sheet: 1.83 (0.35), residues: 236 loop : -0.63 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B1820 HIS 0.020 0.001 HIS A1988 PHE 0.037 0.001 PHE B4164 TYR 0.016 0.001 TYR B1457 ARG 0.003 0.000 ARG A1382 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1651) hydrogen bonds : angle 3.45116 ( 4851) covalent geometry : bond 0.00275 (31441) covalent geometry : angle 0.53765 (42706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 3.363 Fit side-chains REVERT: A 1856 MET cc_start: 0.8635 (tpt) cc_final: 0.8193 (tpp) REVERT: A 3561 MET cc_start: 0.8251 (mtm) cc_final: 0.7994 (mtt) REVERT: A 3699 MET cc_start: 0.8656 (tpp) cc_final: 0.8273 (tpp) REVERT: A 3816 MET cc_start: 0.8042 (mmt) cc_final: 0.7821 (mmt) REVERT: B 1455 LEU cc_start: 0.8499 (mm) cc_final: 0.8254 (mm) REVERT: B 1875 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5367 (pp) REVERT: B 1917 MET cc_start: 0.7804 (mmp) cc_final: 0.7312 (mmp) REVERT: B 3718 LEU cc_start: 0.8733 (tt) cc_final: 0.8269 (mt) REVERT: B 3848 MET cc_start: 0.9437 (ptp) cc_final: 0.9182 (ptp) REVERT: B 3975 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8557 (tp-100) REVERT: B 4077 MET cc_start: 0.8606 (mmp) cc_final: 0.8295 (mmm) outliers start: 18 outliers final: 13 residues processed: 218 average time/residue: 0.3597 time to fit residues: 136.7796 Evaluate side-chains 217 residues out of total 3507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 2781 VAL Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 3463 VAL Chi-restraints excluded: chain A residue 3639 LEU Chi-restraints excluded: chain B residue 1506 VAL Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 1994 LEU Chi-restraints excluded: chain B residue 2851 VAL Chi-restraints excluded: chain B residue 2930 VAL Chi-restraints excluded: chain B residue 3273 GLU Chi-restraints excluded: chain B residue 3385 ILE Chi-restraints excluded: chain B residue 3789 PHE Chi-restraints excluded: chain B residue 3860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 40 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 246 optimal weight: 9.9990 chunk 379 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 305 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3859 HIS A4180 HIS ** B2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.118122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071045 restraints weight = 84649.479| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.87 r_work: 0.2818 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31441 Z= 0.091 Angle : 0.525 15.391 42706 Z= 0.247 Chirality : 0.036 0.240 5226 Planarity : 0.004 0.048 5319 Dihedral : 3.370 24.477 4187 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.26 % Allowed : 14.20 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.14), residues: 3872 helix: 2.74 (0.11), residues: 2282 sheet: 1.93 (0.35), residues: 236 loop : -0.59 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1820 HIS 0.017 0.001 HIS A1988 PHE 0.034 0.001 PHE B4164 TYR 0.014 0.001 TYR B1457 ARG 0.007 0.000 ARG A2823 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 1651) hydrogen bonds : angle 3.37263 ( 4851) covalent geometry : bond 0.00199 (31441) covalent geometry : angle 0.52468 (42706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17699.53 seconds wall clock time: 305 minutes 27.93 seconds (18327.93 seconds total)