Starting phenix.real_space_refine on Thu Sep 18 13:48:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdp_60001/09_2025/8zdp_60001.map" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 48 5.16 5 C 10734 2.51 5 N 2856 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17019 Number of models: 1 Model: "" Number of chains: 3 Chain: "v" Number of atoms: 5673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5673 Classifications: {'peptide': 763} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 738} Chain: "w" Number of atoms: 5673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5673 Classifications: {'peptide': 763} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 738} Chain: "x" Number of atoms: 5673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5673 Classifications: {'peptide': 763} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 738} Time building chain proxies: 3.50, per 1000 atoms: 0.21 Number of scatterers: 17019 At special positions: 0 Unit cell: (100.795, 97.612, 298.141, 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 48 16.00 O 3381 8.00 N 2856 7.00 C 10734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 838.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4086 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 25 sheets defined 23.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'v' and resid 121 through 132 Processing helix chain 'v' and resid 324 through 328 removed outlier: 3.555A pdb=" N LEU v 327 " --> pdb=" O PRO v 324 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL v 328 " --> pdb=" O GLN v 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 324 through 328' Processing helix chain 'v' and resid 330 through 354 Processing helix chain 'v' and resid 360 through 396 Processing helix chain 'v' and resid 396 through 401 removed outlier: 4.857A pdb=" N VAL v 400 " --> pdb=" O ASP v 396 " (cutoff:3.500A) Processing helix chain 'v' and resid 405 through 409 Processing helix chain 'v' and resid 411 through 430 removed outlier: 3.837A pdb=" N LEU v 430 " --> pdb=" O ILE v 426 " (cutoff:3.500A) Processing helix chain 'v' and resid 439 through 476 Processing helix chain 'v' and resid 495 through 501 removed outlier: 4.002A pdb=" N CYS v 499 " --> pdb=" O PRO v 495 " (cutoff:3.500A) Processing helix chain 'v' and resid 653 through 659 Processing helix chain 'v' and resid 663 through 674 Processing helix chain 'w' and resid 121 through 132 Processing helix chain 'w' and resid 149 through 153 Processing helix chain 'w' and resid 324 through 328 removed outlier: 3.520A pdb=" N LEU w 327 " --> pdb=" O PRO w 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL w 328 " --> pdb=" O GLN w 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 324 through 328' Processing helix chain 'w' and resid 330 through 354 Processing helix chain 'w' and resid 360 through 396 Processing helix chain 'w' and resid 396 through 401 removed outlier: 4.727A pdb=" N VAL w 400 " --> pdb=" O ASP w 396 " (cutoff:3.500A) Processing helix chain 'w' and resid 405 through 409 Processing helix chain 'w' and resid 411 through 430 removed outlier: 3.736A pdb=" N LEU w 430 " --> pdb=" O ILE w 426 " (cutoff:3.500A) Processing helix chain 'w' and resid 439 through 476 Processing helix chain 'w' and resid 495 through 500 removed outlier: 3.985A pdb=" N CYS w 499 " --> pdb=" O PRO w 495 " (cutoff:3.500A) Processing helix chain 'w' and resid 653 through 659 Processing helix chain 'w' and resid 663 through 674 Processing helix chain 'x' and resid 121 through 132 Processing helix chain 'x' and resid 324 through 328 removed outlier: 3.614A pdb=" N LEU x 327 " --> pdb=" O PRO x 324 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL x 328 " --> pdb=" O GLN x 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 324 through 328' Processing helix chain 'x' and resid 330 through 354 Processing helix chain 'x' and resid 360 through 396 Processing helix chain 'x' and resid 396 through 401 removed outlier: 4.696A pdb=" N VAL x 400 " --> pdb=" O ASP x 396 " (cutoff:3.500A) Processing helix chain 'x' and resid 405 through 409 Processing helix chain 'x' and resid 411 through 430 removed outlier: 3.835A pdb=" N LEU x 430 " --> pdb=" O ILE x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 439 through 476 Processing helix chain 'x' and resid 495 through 501 removed outlier: 4.190A pdb=" N CYS x 499 " --> pdb=" O PRO x 495 " (cutoff:3.500A) Processing helix chain 'x' and resid 653 through 659 Processing helix chain 'x' and resid 663 through 674 Processing sheet with id=AA1, first strand: chain 'v' and resid 186 through 189 Processing sheet with id=AA2, first strand: chain 'v' and resid 210 through 213 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 210 through 213 current: chain 'v' and resid 265 through 268 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'v' and resid 224 through 236 Processing sheet with id=AA4, first strand: chain 'v' and resid 490 through 492 Processing sheet with id=AA5, first strand: chain 'v' and resid 503 through 507 removed outlier: 5.792A pdb=" N GLY v 526 " --> pdb=" O LEU v 505 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 526 through 529 current: chain 'v' and resid 601 through 613 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 601 through 613 current: chain 'v' and resid 676 through 678 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 676 through 678 current: chain 'w' and resid 526 through 529 removed outlier: 5.789A pdb=" N GLY x 526 " --> pdb=" O LEU x 505 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'v' and resid 648 through 651 removed outlier: 3.884A pdb=" N GLY v 543 " --> pdb=" O VAL v 621 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG v 618 " --> pdb=" O GLU v 578 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL v 575 " --> pdb=" O GLY v 588 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY v 588 " --> pdb=" O VAL v 575 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG v 577 " --> pdb=" O SER v 586 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER v 586 " --> pdb=" O ARG v 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'v' and resid 694 through 696 removed outlier: 4.461A pdb=" N TRP v 872 " --> pdb=" O GLU v 751 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU v 751 " --> pdb=" O TRP v 872 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU v 874 " --> pdb=" O TRP v 749 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP v 749 " --> pdb=" O LEU v 874 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN v 748 " --> pdb=" O PHE v 818 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU v 836 " --> pdb=" O VAL v 827 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS v 829 " --> pdb=" O SER v 834 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER v 834 " --> pdb=" O LYS v 829 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'v' and resid 707 through 711 removed outlier: 5.186A pdb=" N GLY v 854 " --> pdb=" O TYR v 739 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE v 853 " --> pdb=" O ALA v 772 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY v 855 " --> pdb=" O MET v 770 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N MET v 770 " --> pdb=" O GLY v 855 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG v 857 " --> pdb=" O LEU v 768 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU v 768 " --> pdb=" O ARG v 857 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER v 859 " --> pdb=" O GLU v 766 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU v 766 " --> pdb=" O SER v 859 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU v 766 " --> pdb=" O VAL v 784 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU v 768 " --> pdb=" O LEU v 782 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA v 803 " --> pdb=" O ILE v 791 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR v 793 " --> pdb=" O GLU v 801 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU v 801 " --> pdb=" O THR v 793 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'v' and resid 718 through 721 Processing sheet with id=AB1, first strand: chain 'w' and resid 186 through 189 Processing sheet with id=AB2, first strand: chain 'w' and resid 210 through 212 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 210 through 212 current: chain 'w' and resid 294 through 301 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'w' and resid 275 through 288 removed outlier: 7.791A pdb=" N THR w 276 " --> pdb=" O GLY w 237 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY w 237 " --> pdb=" O THR w 276 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP w 278 " --> pdb=" O TYR w 235 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR w 235 " --> pdb=" O ASP w 278 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL w 288 " --> pdb=" O GLN w 225 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN w 225 " --> pdb=" O VAL w 288 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TRP w 232 " --> pdb=" O ASP w 314 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASP w 314 " --> pdb=" O TRP w 232 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS w 234 " --> pdb=" O PHE w 312 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE w 312 " --> pdb=" O LYS w 234 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER w 236 " --> pdb=" O VAL w 310 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL w 310 " --> pdb=" O SER w 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'w' and resid 490 through 492 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 490 through 492 current: chain 'w' and resid 601 through 613 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 601 through 613 current: chain 'w' and resid 676 through 678 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'w' and resid 584 through 591 removed outlier: 5.635A pdb=" N SER w 586 " --> pdb=" O ARG w 577 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG w 577 " --> pdb=" O SER w 586 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY w 588 " --> pdb=" O VAL w 575 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG w 618 " --> pdb=" O GLU w 578 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY w 543 " --> pdb=" O VAL w 621 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'w' and resid 694 through 696 removed outlier: 4.435A pdb=" N TRP w 872 " --> pdb=" O GLU w 751 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU w 751 " --> pdb=" O TRP w 872 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU w 874 " --> pdb=" O TRP w 749 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP w 749 " --> pdb=" O LEU w 874 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN w 748 " --> pdb=" O PHE w 818 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU w 836 " --> pdb=" O VAL w 827 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS w 829 " --> pdb=" O SER w 834 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER w 834 " --> pdb=" O LYS w 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'w' and resid 707 through 711 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 733 through 739 current: chain 'w' and resid 779 through 784 removed outlier: 6.803A pdb=" N ALA w 789 " --> pdb=" O SER w 804 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER w 804 " --> pdb=" O ALA w 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE w 791 " --> pdb=" O ARG w 802 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 800 through 806 current: chain 'w' and resid 864 through 865 Processing sheet with id=AB8, first strand: chain 'w' and resid 718 through 721 Processing sheet with id=AB9, first strand: chain 'x' and resid 186 through 189 Processing sheet with id=AC1, first strand: chain 'x' and resid 210 through 212 WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 210 through 212 current: chain 'x' and resid 294 through 301 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'x' and resid 224 through 236 Processing sheet with id=AC3, first strand: chain 'x' and resid 490 through 492 WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 490 through 492 current: chain 'x' and resid 601 through 613 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'x' and resid 648 through 651 removed outlier: 3.604A pdb=" N GLY x 543 " --> pdb=" O VAL x 621 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG x 618 " --> pdb=" O GLU x 578 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY x 588 " --> pdb=" O VAL x 575 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG x 577 " --> pdb=" O SER x 586 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER x 586 " --> pdb=" O ARG x 577 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'x' and resid 694 through 696 removed outlier: 4.434A pdb=" N TRP x 872 " --> pdb=" O GLU x 751 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU x 751 " --> pdb=" O TRP x 872 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU x 874 " --> pdb=" O TRP x 749 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP x 749 " --> pdb=" O LEU x 874 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU x 836 " --> pdb=" O VAL x 827 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS x 829 " --> pdb=" O SER x 834 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER x 834 " --> pdb=" O LYS x 829 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'x' and resid 707 through 711 removed outlier: 5.117A pdb=" N GLY x 854 " --> pdb=" O TYR x 739 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE x 853 " --> pdb=" O ALA x 772 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY x 855 " --> pdb=" O MET x 770 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N MET x 770 " --> pdb=" O GLY x 855 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG x 857 " --> pdb=" O LEU x 768 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU x 768 " --> pdb=" O ARG x 857 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER x 859 " --> pdb=" O GLU x 766 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU x 766 " --> pdb=" O SER x 859 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU x 766 " --> pdb=" O VAL x 784 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU x 768 " --> pdb=" O LEU x 782 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA x 789 " --> pdb=" O SER x 804 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER x 804 " --> pdb=" O ALA x 789 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE x 791 " --> pdb=" O ARG x 802 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'x' and resid 718 through 721 616 hydrogen bonds defined for protein. 1731 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: 3.50 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5663 1.34 - 1.46: 3528 1.46 - 1.57: 8068 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 17346 Sorted by residual: bond pdb=" N LEU w 535 " pdb=" CA LEU w 535 " ideal model delta sigma weight residual 1.457 1.439 0.018 1.41e-02 5.03e+03 1.56e+00 bond pdb=" CA GLN w 225 " pdb=" CB GLN w 225 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.13e-01 bond pdb=" N THR v 862 " pdb=" CA THR v 862 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 6.58e-01 bond pdb=" N THR w 862 " pdb=" CA THR w 862 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 6.22e-01 bond pdb=" N THR x 862 " pdb=" CA THR x 862 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 6.00e-01 ... (remaining 17341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 23097 1.29 - 2.58: 484 2.58 - 3.87: 98 3.87 - 5.15: 8 5.15 - 6.44: 7 Bond angle restraints: 23694 Sorted by residual: angle pdb=" C SER v 246 " pdb=" CA SER v 246 " pdb=" CB SER v 246 " ideal model delta sigma weight residual 110.42 116.17 -5.75 1.99e+00 2.53e-01 8.36e+00 angle pdb=" CA GLN w 225 " pdb=" CB GLN w 225 " pdb=" CG GLN w 225 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.10e+00 angle pdb=" N THR v 208 " pdb=" CA THR v 208 " pdb=" C THR v 208 " ideal model delta sigma weight residual 109.18 112.89 -3.71 1.42e+00 4.96e-01 6.83e+00 angle pdb=" C ALA w 861 " pdb=" N THR w 862 " pdb=" CA THR w 862 " ideal model delta sigma weight residual 122.46 125.74 -3.28 1.41e+00 5.03e-01 5.40e+00 angle pdb=" C ALA v 861 " pdb=" N THR v 862 " pdb=" CA THR v 862 " ideal model delta sigma weight residual 122.46 125.68 -3.22 1.41e+00 5.03e-01 5.23e+00 ... (remaining 23689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 9209 17.38 - 34.76: 686 34.76 - 52.14: 120 52.14 - 69.52: 26 69.52 - 86.90: 15 Dihedral angle restraints: 10056 sinusoidal: 3624 harmonic: 6432 Sorted by residual: dihedral pdb=" CA ASP x 182 " pdb=" CB ASP x 182 " pdb=" CG ASP x 182 " pdb=" OD1 ASP x 182 " ideal model delta sinusoidal sigma weight residual -30.00 -88.97 58.97 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP v 182 " pdb=" CB ASP v 182 " pdb=" CG ASP v 182 " pdb=" OD1 ASP v 182 " ideal model delta sinusoidal sigma weight residual -30.00 -87.46 57.46 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG ARG w 624 " pdb=" CD ARG w 624 " pdb=" NE ARG w 624 " pdb=" CZ ARG w 624 " ideal model delta sinusoidal sigma weight residual 180.00 135.57 44.43 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 10053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1724 0.028 - 0.056: 631 0.056 - 0.084: 234 0.084 - 0.112: 168 0.112 - 0.140: 42 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA VAL v 180 " pdb=" N VAL v 180 " pdb=" C VAL v 180 " pdb=" CB VAL v 180 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE v 219 " pdb=" N ILE v 219 " pdb=" C ILE v 219 " pdb=" CB ILE v 219 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE x 858 " pdb=" N ILE x 858 " pdb=" C ILE x 858 " pdb=" CB ILE x 858 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 2796 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE v 494 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO v 495 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO v 495 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO v 495 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY v 215 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO v 216 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO v 216 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO v 216 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY w 215 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO w 216 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO w 216 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO w 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 483 2.69 - 3.24: 17702 3.24 - 3.80: 28240 3.80 - 4.35: 35626 4.35 - 4.90: 58952 Nonbonded interactions: 141003 Sorted by model distance: nonbonded pdb=" ND1 HIS v 160 " pdb=" O PRO x 154 " model vdw 2.138 3.120 nonbonded pdb=" OG1 THR v 663 " pdb=" OE1 GLU v 666 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR w 757 " pdb=" O ASN w 810 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR w 663 " pdb=" OE1 GLU w 666 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR x 663 " pdb=" OE1 GLU x 666 " model vdw 2.162 3.040 ... (remaining 140998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.002 0.029 17346 Z= 0.113 Angle : 0.484 6.442 23694 Z= 0.257 Chirality : 0.041 0.140 2799 Planarity : 0.003 0.044 3054 Dihedral : 13.334 86.901 5970 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2283 helix: 3.22 (0.22), residues: 483 sheet: -0.07 (0.22), residues: 567 loop : -1.61 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 296 TYR 0.006 0.001 TYR v 235 PHE 0.020 0.001 PHE v 372 TRP 0.013 0.001 TRP x 375 HIS 0.004 0.001 HIS x 520 Details of bonding type rmsd covalent geometry : bond 0.00231 (17346) covalent geometry : angle 0.48411 (23694) hydrogen bonds : bond 0.08495 ( 616) hydrogen bonds : angle 4.79918 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5531 (ppp) cc_final: 0.3903 (mmt) REVERT: v 492 VAL cc_start: 0.9292 (p) cc_final: 0.8972 (p) REVERT: v 558 MET cc_start: 0.8092 (mtp) cc_final: 0.7737 (mtp) REVERT: v 681 MET cc_start: 0.8608 (mmm) cc_final: 0.8331 (tpp) REVERT: v 775 ASP cc_start: 0.8826 (m-30) cc_final: 0.8445 (t0) REVERT: v 796 TRP cc_start: 0.8496 (p90) cc_final: 0.8036 (p90) REVERT: w 147 LEU cc_start: 0.8403 (mt) cc_final: 0.8081 (pt) REVERT: w 212 LEU cc_start: 0.8105 (tp) cc_final: 0.7840 (tp) REVERT: w 297 LEU cc_start: 0.8600 (tp) cc_final: 0.8241 (pp) REVERT: w 707 TRP cc_start: 0.9518 (m100) cc_final: 0.9014 (m100) REVERT: w 751 GLU cc_start: 0.8481 (pt0) cc_final: 0.8264 (pt0) REVERT: w 770 MET cc_start: 0.7074 (pmm) cc_final: 0.6767 (pmm) REVERT: w 796 TRP cc_start: 0.8794 (p90) cc_final: 0.8481 (p90) REVERT: x 143 MET cc_start: 0.5697 (ppp) cc_final: 0.5492 (ppp) REVERT: x 186 TRP cc_start: 0.7413 (m100) cc_final: 0.7123 (m100) REVERT: x 232 TRP cc_start: 0.6927 (m-10) cc_final: 0.6714 (m-10) REVERT: x 327 LEU cc_start: 0.8638 (mt) cc_final: 0.7850 (pp) REVERT: x 363 ASP cc_start: 0.8783 (m-30) cc_final: 0.8532 (m-30) REVERT: x 396 ASP cc_start: 0.8305 (t70) cc_final: 0.7812 (m-30) REVERT: x 497 MET cc_start: 0.8783 (ppp) cc_final: 0.8529 (ppp) REVERT: x 796 TRP cc_start: 0.8534 (p90) cc_final: 0.8194 (p90) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1367 time to fit residues: 61.5004 Evaluate side-chains 159 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0050 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 171 ASN v 470 GLN v 847 HIS w 281 GLN x 717 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064913 restraints weight = 64252.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066693 restraints weight = 37417.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067922 restraints weight = 25219.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068741 restraints weight = 18881.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069231 restraints weight = 15392.186| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17346 Z= 0.115 Angle : 0.507 10.469 23694 Z= 0.266 Chirality : 0.041 0.149 2799 Planarity : 0.003 0.042 3054 Dihedral : 3.782 15.017 2415 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2283 helix: 3.18 (0.22), residues: 483 sheet: -0.37 (0.22), residues: 555 loop : -1.54 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG v 852 TYR 0.011 0.001 TYR v 286 PHE 0.031 0.001 PHE x 694 TRP 0.009 0.001 TRP x 375 HIS 0.007 0.001 HIS x 160 Details of bonding type rmsd covalent geometry : bond 0.00257 (17346) covalent geometry : angle 0.50704 (23694) hydrogen bonds : bond 0.03427 ( 616) hydrogen bonds : angle 4.34404 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.4800 (ppp) cc_final: 0.3749 (mmt) REVERT: v 212 LEU cc_start: 0.8252 (tt) cc_final: 0.7992 (tt) REVERT: v 505 LEU cc_start: 0.8679 (mt) cc_final: 0.8340 (mp) REVERT: v 812 VAL cc_start: 0.9477 (m) cc_final: 0.9199 (p) REVERT: w 147 LEU cc_start: 0.8196 (mt) cc_final: 0.7848 (pt) REVERT: w 297 LEU cc_start: 0.8377 (tp) cc_final: 0.8172 (pp) REVERT: w 638 MET cc_start: 0.8066 (tmm) cc_final: 0.7708 (tmm) REVERT: w 707 TRP cc_start: 0.9408 (m100) cc_final: 0.9060 (m100) REVERT: x 319 LYS cc_start: 0.7390 (mttp) cc_final: 0.6579 (mttp) REVERT: x 396 ASP cc_start: 0.8177 (t70) cc_final: 0.7674 (m-30) REVERT: x 497 MET cc_start: 0.8817 (ppp) cc_final: 0.8599 (ppp) REVERT: x 545 ILE cc_start: 0.9473 (tt) cc_final: 0.8609 (tt) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1330 time to fit residues: 42.8919 Evaluate side-chains 135 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 170 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 189 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 771 HIS v 847 HIS ** x 771 HIS ** 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 = 0.3518 r_free = 0.3518 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064093 restraints weight = 65289.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065851 restraints weight = 38048.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067042 restraints weight = 25750.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067873 restraints weight = 19497.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068431 restraints weight = 15887.538| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17346 Z= 0.124 Angle : 0.504 8.700 23694 Z= 0.263 Chirality : 0.041 0.147 2799 Planarity : 0.003 0.041 3054 Dihedral : 3.836 20.674 2415 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2283 helix: 3.06 (0.22), residues: 483 sheet: -0.38 (0.22), residues: 531 loop : -1.58 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG w 624 TYR 0.013 0.001 TYR w 572 PHE 0.016 0.001 PHE w 694 TRP 0.013 0.001 TRP v 679 HIS 0.007 0.001 HIS v 160 Details of bonding type rmsd covalent geometry : bond 0.00278 (17346) covalent geometry : angle 0.50439 (23694) hydrogen bonds : bond 0.03289 ( 616) hydrogen bonds : angle 4.22840 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.4975 (ppp) cc_final: 0.4219 (mmt) REVERT: v 343 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7484 (mt-10) REVERT: v 535 LEU cc_start: 0.8288 (tp) cc_final: 0.8064 (tp) REVERT: v 682 MET cc_start: 0.8828 (mtp) cc_final: 0.8534 (mtp) REVERT: v 812 VAL cc_start: 0.9481 (m) cc_final: 0.9176 (p) REVERT: w 147 LEU cc_start: 0.8216 (mt) cc_final: 0.7766 (pt) REVERT: w 297 LEU cc_start: 0.8454 (tp) cc_final: 0.8241 (pp) REVERT: w 497 MET cc_start: 0.8648 (ppp) cc_final: 0.8300 (ppp) REVERT: w 638 MET cc_start: 0.7589 (tmm) cc_final: 0.7200 (tmm) REVERT: w 707 TRP cc_start: 0.9449 (m100) cc_final: 0.9069 (m100) REVERT: x 156 LEU cc_start: 0.8056 (mm) cc_final: 0.7759 (mm) REVERT: x 288 VAL cc_start: 0.7499 (t) cc_final: 0.7272 (t) REVERT: x 327 LEU cc_start: 0.8142 (mt) cc_final: 0.7193 (pp) REVERT: x 343 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7907 (mm-30) REVERT: x 396 ASP cc_start: 0.8204 (t70) cc_final: 0.7677 (m-30) REVERT: x 497 MET cc_start: 0.8854 (ppp) cc_final: 0.8613 (ppp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1256 time to fit residues: 36.8998 Evaluate side-chains 127 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 456 GLN ** x 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064303 restraints weight = 65194.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066029 restraints weight = 38442.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067227 restraints weight = 26222.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067998 restraints weight = 19862.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068575 restraints weight = 16336.932| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17346 Z= 0.114 Angle : 0.495 8.045 23694 Z= 0.259 Chirality : 0.041 0.141 2799 Planarity : 0.003 0.042 3054 Dihedral : 3.836 18.644 2415 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.18), residues: 2283 helix: 3.06 (0.22), residues: 483 sheet: -0.30 (0.22), residues: 543 loop : -1.63 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG v 741 TYR 0.021 0.001 TYR v 286 PHE 0.021 0.001 PHE w 694 TRP 0.031 0.001 TRP w 186 HIS 0.006 0.001 HIS w 160 Details of bonding type rmsd covalent geometry : bond 0.00255 (17346) covalent geometry : angle 0.49470 (23694) hydrogen bonds : bond 0.03202 ( 616) hydrogen bonds : angle 4.17256 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5131 (ppp) cc_final: 0.4242 (mmt) REVERT: v 343 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7486 (mt-10) REVERT: v 638 MET cc_start: 0.7702 (ttt) cc_final: 0.7144 (ttt) REVERT: v 677 MET cc_start: 0.8500 (tmm) cc_final: 0.8286 (tmm) REVERT: v 812 VAL cc_start: 0.9465 (m) cc_final: 0.9180 (p) REVERT: w 139 LEU cc_start: 0.7633 (tt) cc_final: 0.6834 (tt) REVERT: w 147 LEU cc_start: 0.8187 (mt) cc_final: 0.7707 (pt) REVERT: w 186 TRP cc_start: 0.7127 (m100) cc_final: 0.6868 (m100) REVERT: w 296 ARG cc_start: 0.5001 (mtt180) cc_final: 0.4678 (mtt-85) REVERT: w 297 LEU cc_start: 0.8567 (tp) cc_final: 0.8255 (pp) REVERT: w 343 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7769 (mp0) REVERT: w 497 MET cc_start: 0.8629 (ppp) cc_final: 0.8197 (ppp) REVERT: w 638 MET cc_start: 0.7997 (tmm) cc_final: 0.7639 (tmm) REVERT: w 739 TYR cc_start: 0.8439 (t80) cc_final: 0.7552 (t80) REVERT: x 139 LEU cc_start: 0.8016 (mp) cc_final: 0.7676 (tt) REVERT: x 143 MET cc_start: 0.4869 (ppp) cc_final: 0.4045 (mmt) REVERT: x 396 ASP cc_start: 0.8270 (t70) cc_final: 0.7715 (m-30) REVERT: x 497 MET cc_start: 0.8898 (ppp) cc_final: 0.8624 (ppp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1271 time to fit residues: 35.5301 Evaluate side-chains 125 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 470 GLN w 281 GLN w 832 GLN x 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061511 restraints weight = 65860.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063206 restraints weight = 38979.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064349 restraints weight = 26691.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065145 restraints weight = 20396.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.065624 restraints weight = 16823.226| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17346 Z= 0.176 Angle : 0.534 6.995 23694 Z= 0.280 Chirality : 0.042 0.158 2799 Planarity : 0.004 0.047 3054 Dihedral : 4.042 18.398 2415 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2283 helix: 2.99 (0.23), residues: 483 sheet: -0.34 (0.22), residues: 570 loop : -1.72 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG w 624 TYR 0.014 0.001 TYR x 781 PHE 0.019 0.002 PHE v 372 TRP 0.017 0.001 TRP v 679 HIS 0.010 0.002 HIS x 771 Details of bonding type rmsd covalent geometry : bond 0.00390 (17346) covalent geometry : angle 0.53362 (23694) hydrogen bonds : bond 0.03427 ( 616) hydrogen bonds : angle 4.31583 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.4978 (ppp) cc_final: 0.4167 (mmt) REVERT: v 535 LEU cc_start: 0.8221 (tp) cc_final: 0.7979 (tp) REVERT: v 638 MET cc_start: 0.7621 (ttt) cc_final: 0.7319 (ttt) REVERT: v 677 MET cc_start: 0.8499 (tmm) cc_final: 0.8181 (tmm) REVERT: v 812 VAL cc_start: 0.9510 (m) cc_final: 0.9250 (p) REVERT: v 859 SER cc_start: 0.8951 (m) cc_final: 0.8314 (p) REVERT: w 139 LEU cc_start: 0.7487 (tt) cc_final: 0.7169 (tt) REVERT: w 147 LEU cc_start: 0.8324 (mt) cc_final: 0.7873 (pt) REVERT: w 186 TRP cc_start: 0.7390 (m100) cc_final: 0.7123 (m100) REVERT: w 343 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7855 (mp0) REVERT: w 638 MET cc_start: 0.8120 (tmm) cc_final: 0.7676 (tmm) REVERT: w 739 TYR cc_start: 0.8687 (t80) cc_final: 0.7591 (t80) REVERT: x 139 LEU cc_start: 0.7970 (mp) cc_final: 0.7566 (mp) REVERT: x 343 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7507 (mt-10) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1389 time to fit residues: 36.9950 Evaluate side-chains 116 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 470 GLN w 281 GLN ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 456 GLN x 470 GLN ** x 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062411 restraints weight = 65715.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064079 restraints weight = 38869.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.065251 restraints weight = 26762.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066050 restraints weight = 20430.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066581 restraints weight = 16805.637| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17346 Z= 0.133 Angle : 0.520 9.073 23694 Z= 0.269 Chirality : 0.042 0.146 2799 Planarity : 0.004 0.045 3054 Dihedral : 3.994 19.144 2415 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2283 helix: 2.88 (0.23), residues: 483 sheet: -0.31 (0.22), residues: 543 loop : -1.73 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG w 624 TYR 0.011 0.001 TYR w 739 PHE 0.024 0.001 PHE w 372 TRP 0.011 0.001 TRP w 186 HIS 0.004 0.001 HIS w 771 Details of bonding type rmsd covalent geometry : bond 0.00300 (17346) covalent geometry : angle 0.51997 (23694) hydrogen bonds : bond 0.03291 ( 616) hydrogen bonds : angle 4.23823 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 212 LEU cc_start: 0.8125 (tt) cc_final: 0.7900 (tt) REVERT: v 535 LEU cc_start: 0.8263 (tp) cc_final: 0.8010 (tp) REVERT: v 812 VAL cc_start: 0.9489 (m) cc_final: 0.9227 (p) REVERT: v 859 SER cc_start: 0.8973 (m) cc_final: 0.8385 (p) REVERT: w 147 LEU cc_start: 0.8344 (mt) cc_final: 0.7909 (pt) REVERT: w 186 TRP cc_start: 0.7390 (m100) cc_final: 0.7150 (m100) REVERT: w 343 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7863 (mp0) REVERT: w 638 MET cc_start: 0.8108 (tmm) cc_final: 0.7732 (tmm) REVERT: w 739 TYR cc_start: 0.8676 (t80) cc_final: 0.7573 (t80) REVERT: x 143 MET cc_start: 0.5371 (ppp) cc_final: 0.5143 (ppp) REVERT: x 232 TRP cc_start: 0.7376 (m-10) cc_final: 0.7143 (m-10) REVERT: x 343 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7807 (mp0) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1324 time to fit residues: 34.7289 Evaluate side-chains 114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 72 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 186 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.081922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.063000 restraints weight = 65078.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064690 restraints weight = 38409.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065844 restraints weight = 26351.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066644 restraints weight = 20036.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067032 restraints weight = 16481.243| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17346 Z= 0.123 Angle : 0.515 8.269 23694 Z= 0.266 Chirality : 0.042 0.149 2799 Planarity : 0.003 0.046 3054 Dihedral : 3.942 20.104 2415 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2283 helix: 2.88 (0.23), residues: 483 sheet: -0.29 (0.22), residues: 564 loop : -1.78 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG w 624 TYR 0.011 0.001 TYR w 739 PHE 0.045 0.002 PHE v 132 TRP 0.012 0.001 TRP v 679 HIS 0.004 0.001 HIS w 771 Details of bonding type rmsd covalent geometry : bond 0.00274 (17346) covalent geometry : angle 0.51522 (23694) hydrogen bonds : bond 0.03237 ( 616) hydrogen bonds : angle 4.21015 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5274 (ppp) cc_final: 0.4467 (mmt) REVERT: v 147 LEU cc_start: 0.7457 (tp) cc_final: 0.7223 (tp) REVERT: v 770 MET cc_start: 0.7603 (ttp) cc_final: 0.7333 (ttp) REVERT: v 812 VAL cc_start: 0.9465 (m) cc_final: 0.9217 (p) REVERT: v 859 SER cc_start: 0.8985 (m) cc_final: 0.8388 (p) REVERT: w 147 LEU cc_start: 0.8335 (mt) cc_final: 0.7853 (pt) REVERT: w 186 TRP cc_start: 0.7376 (m100) cc_final: 0.7050 (m100) REVERT: w 296 ARG cc_start: 0.4775 (mtt180) cc_final: 0.4499 (mtt-85) REVERT: w 343 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7842 (mp0) REVERT: w 638 MET cc_start: 0.8109 (tmm) cc_final: 0.7767 (tmm) REVERT: w 739 TYR cc_start: 0.8717 (t80) cc_final: 0.7614 (t80) REVERT: x 139 LEU cc_start: 0.7701 (mp) cc_final: 0.7092 (mt) REVERT: x 232 TRP cc_start: 0.7370 (m-10) cc_final: 0.7160 (m-10) REVERT: x 288 VAL cc_start: 0.7549 (t) cc_final: 0.7330 (t) REVERT: x 489 THR cc_start: 0.9067 (m) cc_final: 0.8684 (p) REVERT: x 497 MET cc_start: 0.8878 (ppp) cc_final: 0.8601 (ppp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1443 time to fit residues: 37.5424 Evaluate side-chains 117 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062665 restraints weight = 65791.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064356 restraints weight = 38983.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065515 restraints weight = 26704.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066266 restraints weight = 20326.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066843 restraints weight = 16753.011| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17346 Z= 0.134 Angle : 0.538 7.818 23694 Z= 0.276 Chirality : 0.042 0.162 2799 Planarity : 0.004 0.047 3054 Dihedral : 3.973 21.558 2415 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2283 helix: 2.82 (0.23), residues: 483 sheet: -0.22 (0.22), residues: 579 loop : -1.83 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG v 774 TYR 0.011 0.001 TYR w 739 PHE 0.026 0.002 PHE v 132 TRP 0.064 0.001 TRP w 279 HIS 0.004 0.001 HIS x 520 Details of bonding type rmsd covalent geometry : bond 0.00307 (17346) covalent geometry : angle 0.53826 (23694) hydrogen bonds : bond 0.03295 ( 616) hydrogen bonds : angle 4.24462 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5073 (ppp) cc_final: 0.4430 (mmt) REVERT: v 147 LEU cc_start: 0.7475 (tp) cc_final: 0.7223 (tp) REVERT: v 212 LEU cc_start: 0.8058 (tt) cc_final: 0.7797 (tt) REVERT: v 638 MET cc_start: 0.7945 (ttt) cc_final: 0.7613 (tmm) REVERT: v 770 MET cc_start: 0.7639 (ttp) cc_final: 0.7330 (ttp) REVERT: v 812 VAL cc_start: 0.9476 (m) cc_final: 0.9241 (p) REVERT: v 859 SER cc_start: 0.8969 (m) cc_final: 0.8340 (p) REVERT: w 139 LEU cc_start: 0.7784 (tt) cc_final: 0.7431 (tt) REVERT: w 147 LEU cc_start: 0.8415 (mt) cc_final: 0.7906 (pt) REVERT: w 343 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7872 (mp0) REVERT: w 638 MET cc_start: 0.8118 (tmm) cc_final: 0.7842 (tmm) REVERT: w 739 TYR cc_start: 0.8690 (t80) cc_final: 0.7673 (t80) REVERT: x 139 LEU cc_start: 0.7710 (mp) cc_final: 0.7227 (mt) REVERT: x 143 MET cc_start: 0.5365 (ppp) cc_final: 0.4955 (ppp) REVERT: x 497 MET cc_start: 0.8868 (ppp) cc_final: 0.8624 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1436 time to fit residues: 37.3036 Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 281 GLN ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.061212 restraints weight = 66876.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062828 restraints weight = 39845.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063942 restraints weight = 27521.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064667 restraints weight = 21141.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065213 restraints weight = 17583.672| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17346 Z= 0.167 Angle : 0.559 7.674 23694 Z= 0.289 Chirality : 0.042 0.167 2799 Planarity : 0.004 0.045 3054 Dihedral : 4.162 24.034 2415 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.17), residues: 2283 helix: 2.72 (0.23), residues: 483 sheet: -0.27 (0.22), residues: 543 loop : -1.88 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG w 194 TYR 0.012 0.001 TYR x 781 PHE 0.025 0.002 PHE v 372 TRP 0.052 0.001 TRP w 279 HIS 0.005 0.001 HIS w 771 Details of bonding type rmsd covalent geometry : bond 0.00375 (17346) covalent geometry : angle 0.55873 (23694) hydrogen bonds : bond 0.03440 ( 616) hydrogen bonds : angle 4.42133 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5504 (ppp) cc_final: 0.4738 (mmt) REVERT: v 147 LEU cc_start: 0.7813 (tp) cc_final: 0.7548 (tp) REVERT: v 212 LEU cc_start: 0.8244 (tt) cc_final: 0.7981 (tt) REVERT: v 318 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6691 (mmtm) REVERT: v 638 MET cc_start: 0.8148 (ttt) cc_final: 0.7672 (tmm) REVERT: v 677 MET cc_start: 0.8574 (tmm) cc_final: 0.8298 (tmm) REVERT: w 139 LEU cc_start: 0.8024 (tt) cc_final: 0.7810 (tt) REVERT: w 147 LEU cc_start: 0.8593 (mt) cc_final: 0.8100 (pt) REVERT: w 186 TRP cc_start: 0.7450 (m100) cc_final: 0.6918 (m100) REVERT: w 279 TRP cc_start: 0.5787 (m-10) cc_final: 0.5352 (m100) REVERT: w 343 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7921 (mp0) REVERT: w 638 MET cc_start: 0.8180 (tmm) cc_final: 0.7757 (tmm) REVERT: w 739 TYR cc_start: 0.8842 (t80) cc_final: 0.7738 (t80) REVERT: x 139 LEU cc_start: 0.8391 (mp) cc_final: 0.7900 (mt) REVERT: x 143 MET cc_start: 0.5794 (ppp) cc_final: 0.5545 (ppp) REVERT: x 363 ASP cc_start: 0.8730 (m-30) cc_final: 0.8521 (m-30) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1230 time to fit residues: 31.4948 Evaluate side-chains 110 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 220 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062273 restraints weight = 65682.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063918 restraints weight = 38849.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065078 restraints weight = 26763.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065842 restraints weight = 20418.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066404 restraints weight = 16874.358| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17346 Z= 0.130 Angle : 0.540 8.084 23694 Z= 0.277 Chirality : 0.042 0.154 2799 Planarity : 0.004 0.044 3054 Dihedral : 4.084 23.877 2415 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.17), residues: 2283 helix: 2.83 (0.23), residues: 483 sheet: -0.40 (0.22), residues: 552 loop : -1.84 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG v 194 TYR 0.010 0.001 TYR w 561 PHE 0.024 0.002 PHE x 372 TRP 0.040 0.001 TRP w 279 HIS 0.005 0.001 HIS w 771 Details of bonding type rmsd covalent geometry : bond 0.00294 (17346) covalent geometry : angle 0.54015 (23694) hydrogen bonds : bond 0.03239 ( 616) hydrogen bonds : angle 4.28143 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 143 MET cc_start: 0.5306 (ppp) cc_final: 0.4679 (mmt) REVERT: v 147 LEU cc_start: 0.7609 (tp) cc_final: 0.7323 (tp) REVERT: v 232 TRP cc_start: 0.7517 (m-10) cc_final: 0.7090 (m100) REVERT: v 318 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6640 (mmtm) REVERT: v 319 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7263 (mmtt) REVERT: v 638 MET cc_start: 0.8035 (ttt) cc_final: 0.7659 (tmm) REVERT: v 677 MET cc_start: 0.8455 (tmm) cc_final: 0.8254 (tmm) REVERT: v 770 MET cc_start: 0.7777 (ttp) cc_final: 0.6890 (ptm) REVERT: w 147 LEU cc_start: 0.8366 (mt) cc_final: 0.7960 (pt) REVERT: w 186 TRP cc_start: 0.7231 (m100) cc_final: 0.6723 (m100) REVERT: w 343 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7877 (mp0) REVERT: w 638 MET cc_start: 0.8131 (tmm) cc_final: 0.7836 (tmm) REVERT: w 739 TYR cc_start: 0.8714 (t80) cc_final: 0.7759 (t80) REVERT: x 139 LEU cc_start: 0.8212 (mp) cc_final: 0.7884 (mt) REVERT: x 288 VAL cc_start: 0.7627 (t) cc_final: 0.7397 (t) REVERT: x 489 THR cc_start: 0.9089 (m) cc_final: 0.8728 (p) REVERT: x 497 MET cc_start: 0.8880 (ppp) cc_final: 0.8590 (ppp) REVERT: x 632 ARG cc_start: 0.7729 (mtp85) cc_final: 0.6912 (mtt90) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1384 time to fit residues: 35.2996 Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 0.0470 chunk 181 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063085 restraints weight = 65352.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064767 restraints weight = 38330.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065904 restraints weight = 26224.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066697 restraints weight = 19939.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.067136 restraints weight = 16387.385| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17346 Z= 0.114 Angle : 0.532 10.623 23694 Z= 0.271 Chirality : 0.042 0.207 2799 Planarity : 0.004 0.046 3054 Dihedral : 3.989 25.347 2415 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.17), residues: 2283 helix: 2.91 (0.23), residues: 483 sheet: -0.47 (0.22), residues: 561 loop : -1.76 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 296 TYR 0.009 0.001 TYR w 739 PHE 0.022 0.001 PHE x 372 TRP 0.025 0.001 TRP v 679 HIS 0.008 0.001 HIS w 160 Details of bonding type rmsd covalent geometry : bond 0.00256 (17346) covalent geometry : angle 0.53223 (23694) hydrogen bonds : bond 0.03106 ( 616) hydrogen bonds : angle 4.17245 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.05 seconds wall clock time: 56 minutes 5.15 seconds (3365.15 seconds total)