Starting phenix.real_space_refine on Sat Aug 23 14:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.map" model { file = "/net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ck1_16689/08_2025/8ck1_16689.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 35 5.16 5 C 7858 2.51 5 N 2132 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12580 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6419 Classifications: {'peptide': 826} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 794} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "F" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Time building chain proxies: 3.40, per 1000 atoms: 0.27 Number of scatterers: 12580 At special positions: 0 Unit cell: (89.1, 120.15, 207.9, 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 35 16.00 O 2555 8.00 N 2132 7.00 C 7858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 34 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 34 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 639.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 26 sheets defined 22.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 4.257A pdb=" N GLY A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.766A pdb=" N ALA A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 310 through 316 removed outlier: 4.079A pdb=" N ARG A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 552 through 555 Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.534A pdb=" N LEU A 769 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 127 removed outlier: 4.056A pdb=" N VAL D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 127 removed outlier: 3.798A pdb=" N VAL B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 102 through 127 removed outlier: 3.511A pdb=" N VAL C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.693A pdb=" N GLY E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 49 removed outlier: 3.507A pdb=" N ARG E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 142 through 163 removed outlier: 4.871A pdb=" N MET E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 164 through 189 Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 28 through 49 removed outlier: 4.215A pdb=" N TYR F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.569A pdb=" N GLU F 98 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 99' Processing helix chain 'F' and resid 142 through 163 removed outlier: 4.628A pdb=" N MET F 159 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Proline residue: F 160 - end of helix Processing helix chain 'F' and resid 164 through 189 Processing helix chain 'F' and resid 198 through 206 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.650A pdb=" N SER A 721 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 64 removed outlier: 5.675A pdb=" N PHE A 61 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A 562 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 63 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 543 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 536 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 532 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS A 549 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE A 530 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.691A pdb=" N GLY A 90 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 93 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.005A pdb=" N HIS A 137 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 145 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP A 156 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 147 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 154 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.784A pdb=" N ILE A 301 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS A 300 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N HIS A 295 " --> pdb=" O HIS A 300 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 205 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG A 320 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 339 Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 395 removed outlier: 3.642A pdb=" N LEU A 399 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 500 Processing sheet with id=AB4, first strand: chain 'A' and resid 578 through 582 removed outlier: 4.416A pdb=" N GLY A 580 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 715 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR A 582 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 713 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 687 " --> pdb=" O HIS A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 596 removed outlier: 7.452A pdb=" N ALA A 648 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 666 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.189A pdb=" N LYS A 672 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 792 through 794 removed outlier: 5.555A pdb=" N ILE A 742 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 825 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 744 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.001A pdb=" N GLU A 787 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AC1, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AC3, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AC4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.929A pdb=" N THR C 82 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 55 through 59 removed outlier: 3.649A pdb=" N ASP E 85 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR E 132 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE E 83 " --> pdb=" O THR E 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 61 through 64 removed outlier: 4.615A pdb=" N ALA E 61 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS E 73 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 122 " --> pdb=" O HIS E 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 55 through 59 removed outlier: 3.766A pdb=" N ASP F 85 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 132 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 83 " --> pdb=" O THR F 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 64 removed outlier: 7.216A pdb=" N LYS F 73 " --> pdb=" O ILE F 63 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1089 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: 2.39 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4241 1.34 - 1.46: 3037 1.46 - 1.59: 5499 1.59 - 1.72: 0 1.72 - 1.85: 59 Bond restraints: 12836 Sorted by residual: bond pdb=" C VAL A 47 " pdb=" N GLN A 48 " ideal model delta sigma weight residual 1.333 1.403 -0.070 1.39e-02 5.18e+03 2.56e+01 bond pdb=" C GLN A 48 " pdb=" N PRO A 49 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.34e-02 1.83e+03 1.52e+01 bond pdb=" N ILE D 87 " pdb=" CA ILE D 87 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" N VAL A 46 " pdb=" CA VAL A 46 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.47e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.21e-02 6.83e+03 7.96e+00 ... (remaining 12831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16921 1.99 - 3.98: 483 3.98 - 5.96: 55 5.96 - 7.95: 9 7.95 - 9.94: 3 Bond angle restraints: 17471 Sorted by residual: angle pdb=" O VAL A 47 " pdb=" C VAL A 47 " pdb=" N GLN A 48 " ideal model delta sigma weight residual 122.57 127.86 -5.29 1.25e+00 6.40e-01 1.79e+01 angle pdb=" C TYR E 38 " pdb=" N ASP E 39 " pdb=" CA ASP E 39 " ideal model delta sigma weight residual 120.44 115.56 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" C GLY C 59 " pdb=" N ASP C 60 " pdb=" CA ASP C 60 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N THR D 51 " pdb=" CA THR D 51 " pdb=" C THR D 51 " ideal model delta sigma weight residual 113.43 108.91 4.52 1.26e+00 6.30e-01 1.29e+01 angle pdb=" N LEU B 95 " pdb=" CA LEU B 95 " pdb=" C LEU B 95 " ideal model delta sigma weight residual 114.56 110.02 4.54 1.27e+00 6.20e-01 1.28e+01 ... (remaining 17466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6579 17.85 - 35.71: 784 35.71 - 53.56: 200 53.56 - 71.41: 37 71.41 - 89.26: 19 Dihedral angle restraints: 7619 sinusoidal: 2974 harmonic: 4645 Sorted by residual: dihedral pdb=" CA ALA A 777 " pdb=" C ALA A 777 " pdb=" N GLU A 778 " pdb=" CA GLU A 778 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP A 408 " pdb=" C TRP A 408 " pdb=" N MET A 409 " pdb=" CA MET A 409 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP C 73 " pdb=" C ASP C 73 " pdb=" N PRO C 74 " pdb=" CA PRO C 74 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1389 0.044 - 0.087: 367 0.087 - 0.131: 160 0.131 - 0.174: 18 0.174 - 0.218: 6 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA LEU A 659 " pdb=" N LEU A 659 " pdb=" C LEU A 659 " pdb=" CB LEU A 659 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE E 205 " pdb=" N ILE E 205 " pdb=" C ILE E 205 " pdb=" CB ILE E 205 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.51e-01 ... (remaining 1937 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 203 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ALA F 203 " -0.057 2.00e-02 2.50e+03 pdb=" O ALA F 203 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN F 204 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 102 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 103 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 104 " 0.016 2.00e-02 2.50e+03 1.50e-02 4.53e+00 pdb=" CG TYR F 104 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR F 104 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR F 104 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR F 104 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 104 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 104 " 0.001 2.00e-02 2.50e+03 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2536 2.77 - 3.30: 12767 3.30 - 3.83: 21314 3.83 - 4.37: 24700 4.37 - 4.90: 41815 Nonbonded interactions: 103132 Sorted by model distance: nonbonded pdb=" O ASP F 207 " pdb=" OD1 ASP F 207 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B 12 " pdb=" O PRO B 22 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 384 " pdb=" N ARG A 385 " model vdw 2.257 3.120 nonbonded pdb=" O GLU E 98 " pdb=" ND2 ASN E 193 " model vdw 2.260 3.120 nonbonded pdb=" O GLY A 590 " pdb=" OG SER A 612 " model vdw 2.267 3.040 ... (remaining 103127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 12838 Z= 0.243 Angle : 0.752 9.938 17475 Z= 0.445 Chirality : 0.047 0.218 1940 Planarity : 0.004 0.062 2322 Dihedral : 16.949 89.264 4647 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.59 % Allowed : 26.21 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.21), residues: 1604 helix: 0.51 (0.32), residues: 278 sheet: -1.80 (0.25), residues: 419 loop : -1.78 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 32 TYR 0.037 0.002 TYR F 104 PHE 0.015 0.002 PHE F 53 TRP 0.025 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00422 (12836) covalent geometry : angle 0.74944 (17471) SS BOND : bond 0.00427 ( 2) SS BOND : angle 3.95646 ( 4) hydrogen bonds : bond 0.21862 ( 429) hydrogen bonds : angle 8.74618 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 326 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 492 GLU cc_start: 0.7998 (tp30) cc_final: 0.6683 (mt-10) REVERT: A 631 ASP cc_start: 0.7167 (m-30) cc_final: 0.6700 (t0) REVERT: D 62 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 68 PHE cc_start: 0.5675 (t80) cc_final: 0.5281 (t80) REVERT: B 67 THR cc_start: 0.8754 (m) cc_final: 0.8500 (t) REVERT: C 92 GLU cc_start: 0.7751 (mp0) cc_final: 0.7532 (mp0) REVERT: C 112 ARG cc_start: 0.8921 (mmt180) cc_final: 0.8534 (mmt180) REVERT: E 4 LYS cc_start: 0.8686 (mttp) cc_final: 0.8217 (mptt) REVERT: E 27 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7260 (mtpt) REVERT: E 79 ASP cc_start: 0.7581 (p0) cc_final: 0.7335 (p0) REVERT: E 94 ASP cc_start: 0.7228 (t70) cc_final: 0.6788 (t70) REVERT: E 144 ASP cc_start: 0.8980 (p0) cc_final: 0.8720 (p0) REVERT: E 204 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7233 (t0) REVERT: F 18 ASP cc_start: 0.8619 (t0) cc_final: 0.8272 (p0) outliers start: 8 outliers final: 2 residues processed: 328 average time/residue: 0.1186 time to fit residues: 55.9279 Evaluate side-chains 274 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 270 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 204 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.0980 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 353 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN C 120 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085216 restraints weight = 35586.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.087326 restraints weight = 16980.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088667 restraints weight = 9698.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089545 restraints weight = 6251.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090108 restraints weight = 4454.119| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12838 Z= 0.230 Angle : 0.644 8.738 17475 Z= 0.340 Chirality : 0.046 0.202 1940 Planarity : 0.005 0.056 2322 Dihedral : 5.182 50.404 1787 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.90 % Allowed : 25.76 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.20), residues: 1604 helix: 0.74 (0.30), residues: 291 sheet: -1.76 (0.24), residues: 437 loop : -1.81 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 75 TYR 0.024 0.002 TYR C 53 PHE 0.014 0.002 PHE D 21 TRP 0.017 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00516 (12836) covalent geometry : angle 0.64238 (17471) SS BOND : bond 0.00476 ( 2) SS BOND : angle 2.73970 ( 4) hydrogen bonds : bond 0.04836 ( 429) hydrogen bonds : angle 6.35126 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 487 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: A 492 GLU cc_start: 0.8178 (tp30) cc_final: 0.7072 (mt-10) REVERT: A 599 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6815 (m) REVERT: A 670 MET cc_start: 0.7614 (mtm) cc_final: 0.7071 (mtm) REVERT: D 111 ASP cc_start: 0.8143 (m-30) cc_final: 0.7863 (m-30) REVERT: B 9 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8124 (ttm-80) REVERT: B 67 THR cc_start: 0.8694 (m) cc_final: 0.8324 (t) REVERT: B 110 PHE cc_start: 0.8193 (t80) cc_final: 0.7894 (t80) REVERT: B 120 GLN cc_start: 0.8562 (mt0) cc_final: 0.8143 (mt0) REVERT: C 98 GLN cc_start: 0.8641 (mp10) cc_final: 0.8393 (mp10) REVERT: C 101 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: C 119 GLN cc_start: 0.8525 (mt0) cc_final: 0.8075 (mp10) REVERT: E 27 LYS cc_start: 0.8501 (mtmm) cc_final: 0.7691 (mtpt) REVERT: E 79 ASP cc_start: 0.7896 (p0) cc_final: 0.7517 (p0) REVERT: E 94 ASP cc_start: 0.7179 (t0) cc_final: 0.6898 (t70) REVERT: E 144 ASP cc_start: 0.9013 (p0) cc_final: 0.8659 (p0) REVERT: E 151 MET cc_start: 0.9215 (mmm) cc_final: 0.9004 (tpp) REVERT: F 4 LYS cc_start: 0.6265 (tmtt) cc_final: 0.4995 (tmtt) REVERT: F 9 ASN cc_start: 0.8072 (m-40) cc_final: 0.7732 (m110) REVERT: F 18 ASP cc_start: 0.8694 (t0) cc_final: 0.8415 (p0) REVERT: F 131 TYR cc_start: 0.7902 (p90) cc_final: 0.7411 (p90) REVERT: F 141 MET cc_start: 0.8812 (pmm) cc_final: 0.8484 (pmm) REVERT: F 156 ASN cc_start: 0.8898 (t0) cc_final: 0.8656 (t0) outliers start: 66 outliers final: 35 residues processed: 311 average time/residue: 0.1079 time to fit residues: 49.9526 Evaluate side-chains 286 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 143 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 113 optimal weight: 50.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085296 restraints weight = 36128.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087419 restraints weight = 17106.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088784 restraints weight = 9759.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089650 restraints weight = 6307.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090255 restraints weight = 4512.077| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12838 Z= 0.203 Angle : 0.609 9.901 17475 Z= 0.321 Chirality : 0.045 0.204 1940 Planarity : 0.004 0.049 2322 Dihedral : 4.736 20.543 1777 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.20 % Allowed : 25.98 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.20), residues: 1604 helix: 1.03 (0.30), residues: 294 sheet: -1.55 (0.25), residues: 405 loop : -1.84 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 660 TYR 0.022 0.002 TYR C 101 PHE 0.013 0.002 PHE F 53 TRP 0.011 0.001 TRP A 216 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00458 (12836) covalent geometry : angle 0.60822 (17471) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.93300 ( 4) hydrogen bonds : bond 0.04505 ( 429) hydrogen bonds : angle 5.96973 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 212 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: A 487 TRP cc_start: 0.8712 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: A 492 GLU cc_start: 0.8013 (tp30) cc_final: 0.7023 (mt-10) REVERT: A 605 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: D 62 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 67 THR cc_start: 0.8598 (m) cc_final: 0.8230 (t) REVERT: B 87 ILE cc_start: 0.9169 (tp) cc_final: 0.8910 (tp) REVERT: B 89 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7590 (mm) REVERT: B 98 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7847 (mm-40) REVERT: B 107 GLU cc_start: 0.7957 (tp30) cc_final: 0.7517 (tp30) REVERT: B 120 GLN cc_start: 0.8260 (mt0) cc_final: 0.7630 (mt0) REVERT: C 6 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7920 (t0) REVERT: C 101 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: C 112 ARG cc_start: 0.8960 (mmt180) cc_final: 0.8441 (mmt180) REVERT: E 14 ASN cc_start: 0.8964 (t0) cc_final: 0.8725 (t0) REVERT: E 27 LYS cc_start: 0.8653 (mtmm) cc_final: 0.7949 (mtpt) REVERT: E 79 ASP cc_start: 0.7870 (p0) cc_final: 0.7465 (p0) REVERT: E 144 ASP cc_start: 0.8999 (p0) cc_final: 0.8619 (p0) REVERT: E 151 MET cc_start: 0.9192 (mmm) cc_final: 0.8899 (tpt) REVERT: F 3 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8611 (p) REVERT: F 9 ASN cc_start: 0.8028 (m-40) cc_final: 0.7749 (m110) REVERT: F 18 ASP cc_start: 0.8717 (t0) cc_final: 0.8424 (p0) REVERT: F 32 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7361 (mtt-85) REVERT: F 131 TYR cc_start: 0.7973 (p90) cc_final: 0.7351 (p90) REVERT: F 156 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8887 (t0) outliers start: 70 outliers final: 48 residues processed: 315 average time/residue: 0.1090 time to fit residues: 51.0215 Evaluate side-chains 312 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 427 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN ** F 36 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.098497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087529 restraints weight = 35598.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089674 restraints weight = 16856.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.091046 restraints weight = 9625.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091880 restraints weight = 6202.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092500 restraints weight = 4502.993| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12838 Z= 0.138 Angle : 0.568 10.255 17475 Z= 0.298 Chirality : 0.044 0.213 1940 Planarity : 0.004 0.043 2322 Dihedral : 4.504 19.939 1777 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.68 % Allowed : 27.10 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.21), residues: 1604 helix: 1.34 (0.30), residues: 290 sheet: -1.38 (0.26), residues: 409 loop : -1.77 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 660 TYR 0.023 0.001 TYR C 101 PHE 0.020 0.001 PHE B 21 TRP 0.011 0.001 TRP A 216 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00313 (12836) covalent geometry : angle 0.56757 (17471) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.46041 ( 4) hydrogen bonds : bond 0.03947 ( 429) hydrogen bonds : angle 5.57864 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.549 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: A 45 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: A 487 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: A 492 GLU cc_start: 0.7713 (tp30) cc_final: 0.6786 (mt-10) REVERT: A 670 MET cc_start: 0.7573 (mtm) cc_final: 0.7025 (mtm) REVERT: D 62 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 9 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8119 (ttm-80) REVERT: B 67 THR cc_start: 0.8567 (m) cc_final: 0.8170 (t) REVERT: B 87 ILE cc_start: 0.9145 (tp) cc_final: 0.8889 (tp) REVERT: B 92 GLU cc_start: 0.7424 (tp30) cc_final: 0.7217 (tp30) REVERT: B 98 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7843 (mm-40) REVERT: B 107 GLU cc_start: 0.7977 (tp30) cc_final: 0.7460 (tp30) REVERT: B 120 GLN cc_start: 0.8164 (mt0) cc_final: 0.7491 (mt0) REVERT: C 48 ILE cc_start: 0.9023 (mm) cc_final: 0.8797 (mt) REVERT: C 91 GLN cc_start: 0.7906 (tt0) cc_final: 0.7705 (pt0) REVERT: C 101 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: E 79 ASP cc_start: 0.7851 (p0) cc_final: 0.7500 (p0) REVERT: E 144 ASP cc_start: 0.8942 (p0) cc_final: 0.8496 (p0) REVERT: E 151 MET cc_start: 0.9143 (mmm) cc_final: 0.8910 (tpt) REVERT: E 205 ILE cc_start: 0.7995 (tp) cc_final: 0.7773 (tp) REVERT: F 18 ASP cc_start: 0.8695 (t0) cc_final: 0.8397 (p0) REVERT: F 131 TYR cc_start: 0.7903 (p90) cc_final: 0.7227 (p90) REVERT: F 156 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8843 (t0) outliers start: 63 outliers final: 39 residues processed: 316 average time/residue: 0.1032 time to fit residues: 48.6545 Evaluate side-chains 295 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 173 GLN F 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085478 restraints weight = 36039.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087561 restraints weight = 17137.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.088899 restraints weight = 9869.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089763 restraints weight = 6404.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090347 restraints weight = 4601.051| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12838 Z= 0.210 Angle : 0.609 10.087 17475 Z= 0.320 Chirality : 0.045 0.218 1940 Planarity : 0.004 0.042 2322 Dihedral : 4.648 20.055 1777 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 6.01 % Allowed : 26.80 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.21), residues: 1604 helix: 1.37 (0.30), residues: 290 sheet: -1.46 (0.25), residues: 413 loop : -1.76 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 47 TYR 0.022 0.002 TYR C 101 PHE 0.014 0.002 PHE B 21 TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00477 (12836) covalent geometry : angle 0.60834 (17471) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.73782 ( 4) hydrogen bonds : bond 0.04276 ( 429) hydrogen bonds : angle 5.64530 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 259 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 199 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8775 (t) REVERT: A 212 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: A 487 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.7543 (m-10) REVERT: A 492 GLU cc_start: 0.7825 (tp30) cc_final: 0.6846 (mt-10) REVERT: A 670 MET cc_start: 0.7611 (mtm) cc_final: 0.7090 (mtm) REVERT: A 776 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: D 62 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 82 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 9 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8135 (ttm-80) REVERT: B 67 THR cc_start: 0.8613 (m) cc_final: 0.8206 (t) REVERT: B 87 ILE cc_start: 0.9173 (tp) cc_final: 0.8934 (tp) REVERT: B 89 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7605 (mm) REVERT: B 92 GLU cc_start: 0.7513 (tp30) cc_final: 0.7181 (tp30) REVERT: B 98 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7969 (mm-40) REVERT: B 107 GLU cc_start: 0.7994 (tp30) cc_final: 0.7564 (tp30) REVERT: B 120 GLN cc_start: 0.8241 (mt0) cc_final: 0.7453 (mt0) REVERT: C 6 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 48 ILE cc_start: 0.9075 (mm) cc_final: 0.8844 (mt) REVERT: C 101 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: E 79 ASP cc_start: 0.7877 (p0) cc_final: 0.7547 (p0) REVERT: E 144 ASP cc_start: 0.8917 (p0) cc_final: 0.8538 (p0) REVERT: F 3 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (p) REVERT: F 9 ASN cc_start: 0.8075 (m-40) cc_final: 0.7812 (m110) REVERT: F 18 ASP cc_start: 0.8738 (t0) cc_final: 0.8413 (p0) REVERT: F 30 GLU cc_start: 0.8380 (mp0) cc_final: 0.8173 (mp0) REVERT: F 32 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7331 (mtt-85) REVERT: F 131 TYR cc_start: 0.7924 (p90) cc_final: 0.7229 (p90) REVERT: F 168 MET cc_start: 0.9186 (ttp) cc_final: 0.8802 (ttp) outliers start: 81 outliers final: 57 residues processed: 316 average time/residue: 0.0904 time to fit residues: 42.7769 Evaluate side-chains 316 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 247 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.084790 restraints weight = 35954.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086912 restraints weight = 17116.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088263 restraints weight = 9786.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089108 restraints weight = 6339.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089681 restraints weight = 4575.037| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12838 Z= 0.251 Angle : 0.654 9.915 17475 Z= 0.345 Chirality : 0.046 0.219 1940 Planarity : 0.004 0.041 2322 Dihedral : 4.870 20.776 1777 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 6.76 % Allowed : 27.10 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.20), residues: 1604 helix: 1.15 (0.30), residues: 286 sheet: -1.51 (0.25), residues: 417 loop : -1.81 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 47 TYR 0.025 0.002 TYR C 53 PHE 0.014 0.002 PHE F 53 TRP 0.016 0.002 TRP F 37 HIS 0.006 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00567 (12836) covalent geometry : angle 0.65109 (17471) SS BOND : bond 0.00277 ( 2) SS BOND : angle 3.87714 ( 4) hydrogen bonds : bond 0.04555 ( 429) hydrogen bonds : angle 5.78223 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 262 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 199 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8701 (t) REVERT: A 466 TYR cc_start: 0.7994 (m-80) cc_final: 0.7625 (m-80) REVERT: A 487 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: A 492 GLU cc_start: 0.7864 (tp30) cc_final: 0.6988 (mt-10) REVERT: A 670 MET cc_start: 0.7547 (mtm) cc_final: 0.7225 (mtm) REVERT: A 776 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: D 62 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 82 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7899 (p) REVERT: B 9 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: B 67 THR cc_start: 0.8688 (m) cc_final: 0.8272 (t) REVERT: B 89 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7705 (mm) REVERT: B 92 GLU cc_start: 0.7519 (tp30) cc_final: 0.7182 (tp30) REVERT: B 98 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8138 (mm-40) REVERT: B 104 GLU cc_start: 0.8025 (mp0) cc_final: 0.7760 (mp0) REVERT: B 107 GLU cc_start: 0.7891 (tp30) cc_final: 0.7423 (tp30) REVERT: B 120 GLN cc_start: 0.8168 (mt0) cc_final: 0.7452 (mt0) REVERT: C 6 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7951 (t0) REVERT: C 9 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7711 (ttp80) REVERT: C 11 GLN cc_start: 0.7801 (tp40) cc_final: 0.7254 (mp10) REVERT: C 48 ILE cc_start: 0.9124 (mm) cc_final: 0.8487 (mt) REVERT: C 91 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: C 101 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: E 79 ASP cc_start: 0.7797 (p0) cc_final: 0.7519 (p0) REVERT: E 144 ASP cc_start: 0.8937 (p0) cc_final: 0.8555 (p0) REVERT: F 18 ASP cc_start: 0.8790 (t0) cc_final: 0.8425 (p0) REVERT: F 32 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7449 (mtt-85) REVERT: F 131 TYR cc_start: 0.7995 (p90) cc_final: 0.7111 (p90) outliers start: 91 outliers final: 64 residues processed: 327 average time/residue: 0.0892 time to fit residues: 43.6387 Evaluate side-chains 326 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** 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 = 0.3339 r_free = 0.3339 target = 0.097911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.087039 restraints weight = 35470.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089169 restraints weight = 16872.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090518 restraints weight = 9665.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091397 restraints weight = 6277.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091995 restraints weight = 4506.679| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12838 Z= 0.164 Angle : 0.608 9.704 17475 Z= 0.320 Chirality : 0.045 0.219 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.655 20.052 1777 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.90 % Allowed : 29.47 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.21), residues: 1604 helix: 1.23 (0.30), residues: 286 sheet: -1.37 (0.25), residues: 423 loop : -1.73 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.023 0.002 TYR C 101 PHE 0.013 0.001 PHE B 110 TRP 0.020 0.001 TRP F 37 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00374 (12836) covalent geometry : angle 0.60642 (17471) SS BOND : bond 0.00495 ( 2) SS BOND : angle 3.22268 ( 4) hydrogen bonds : bond 0.04084 ( 429) hydrogen bonds : angle 5.58336 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: A 54 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 199 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8712 (t) REVERT: A 466 TYR cc_start: 0.8005 (m-80) cc_final: 0.7681 (m-80) REVERT: A 487 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: A 492 GLU cc_start: 0.7615 (tp30) cc_final: 0.7059 (mt-10) REVERT: A 670 MET cc_start: 0.7502 (mtm) cc_final: 0.7212 (mtm) REVERT: B 21 PHE cc_start: 0.9107 (m-80) cc_final: 0.8878 (m-80) REVERT: B 67 THR cc_start: 0.8632 (m) cc_final: 0.8205 (t) REVERT: B 89 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7452 (mm) REVERT: B 92 GLU cc_start: 0.7364 (tp30) cc_final: 0.6883 (tp30) REVERT: B 98 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8063 (mm-40) REVERT: B 107 GLU cc_start: 0.7982 (tp30) cc_final: 0.7505 (tp30) REVERT: B 120 GLN cc_start: 0.8167 (mt0) cc_final: 0.7463 (mt0) REVERT: C 6 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7892 (t0) REVERT: C 9 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7657 (ttp80) REVERT: C 11 GLN cc_start: 0.7632 (tp40) cc_final: 0.7228 (mp10) REVERT: C 48 ILE cc_start: 0.8664 (mm) cc_final: 0.8444 (mt) REVERT: C 91 GLN cc_start: 0.7806 (tt0) cc_final: 0.7593 (pt0) REVERT: C 101 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: E 79 ASP cc_start: 0.7870 (p0) cc_final: 0.7544 (p0) REVERT: E 92 TYR cc_start: 0.8373 (t80) cc_final: 0.7523 (m-80) REVERT: E 144 ASP cc_start: 0.8863 (p0) cc_final: 0.8458 (p0) REVERT: E 151 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8464 (tpp) REVERT: F 4 LYS cc_start: 0.5743 (tmtt) cc_final: 0.5248 (tptp) REVERT: F 9 ASN cc_start: 0.7992 (m-40) cc_final: 0.7745 (m110) REVERT: F 18 ASP cc_start: 0.8710 (t0) cc_final: 0.8369 (p0) REVERT: F 32 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7441 (mtt-85) REVERT: F 75 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8405 (tpt-90) REVERT: F 131 TYR cc_start: 0.7953 (p90) cc_final: 0.7060 (p90) REVERT: F 156 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8542 (t0) outliers start: 66 outliers final: 49 residues processed: 311 average time/residue: 0.1021 time to fit residues: 46.9050 Evaluate side-chains 311 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 36 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086894 restraints weight = 35528.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088996 restraints weight = 16899.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090320 restraints weight = 9614.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091192 restraints weight = 6207.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091708 restraints weight = 4449.976| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12838 Z= 0.165 Angle : 0.614 9.817 17475 Z= 0.322 Chirality : 0.045 0.212 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.593 19.802 1777 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.97 % Allowed : 29.92 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.21), residues: 1604 helix: 1.19 (0.30), residues: 286 sheet: -1.27 (0.26), residues: 416 loop : -1.73 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.025 0.002 TYR C 53 PHE 0.015 0.001 PHE B 110 TRP 0.014 0.001 TRP F 37 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00377 (12836) covalent geometry : angle 0.61220 (17471) SS BOND : bond 0.00149 ( 2) SS BOND : angle 3.06192 ( 4) hydrogen bonds : bond 0.04051 ( 429) hydrogen bonds : angle 5.50368 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: A 54 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 199 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (t) REVERT: A 487 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: A 492 GLU cc_start: 0.7648 (tp30) cc_final: 0.6955 (mt-10) REVERT: A 503 ASP cc_start: 0.8217 (t70) cc_final: 0.7899 (t0) REVERT: A 670 MET cc_start: 0.7493 (mtm) cc_final: 0.7233 (mtm) REVERT: D 23 TYR cc_start: 0.6315 (p90) cc_final: 0.6069 (p90) REVERT: B 20 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.8986 (m) REVERT: B 21 PHE cc_start: 0.9103 (m-80) cc_final: 0.8853 (m-80) REVERT: B 35 VAL cc_start: 0.9029 (t) cc_final: 0.8732 (p) REVERT: B 67 THR cc_start: 0.8643 (m) cc_final: 0.8226 (t) REVERT: B 87 ILE cc_start: 0.9097 (tp) cc_final: 0.8840 (tp) REVERT: B 89 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7511 (mm) REVERT: B 92 GLU cc_start: 0.7384 (tp30) cc_final: 0.6910 (tp30) REVERT: B 98 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8101 (mm-40) REVERT: B 107 GLU cc_start: 0.7990 (tp30) cc_final: 0.7531 (tp30) REVERT: B 120 GLN cc_start: 0.8128 (mt0) cc_final: 0.7459 (mt0) REVERT: C 6 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7853 (t0) REVERT: C 9 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7622 (ttp80) REVERT: C 11 GLN cc_start: 0.7674 (tp40) cc_final: 0.7283 (mp10) REVERT: C 91 GLN cc_start: 0.7802 (tt0) cc_final: 0.7567 (pt0) REVERT: C 101 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: E 79 ASP cc_start: 0.7880 (p0) cc_final: 0.7543 (p0) REVERT: E 92 TYR cc_start: 0.8142 (t80) cc_final: 0.7459 (m-80) REVERT: E 137 ASP cc_start: 0.8373 (t0) cc_final: 0.8163 (t0) REVERT: E 144 ASP cc_start: 0.8854 (p0) cc_final: 0.8478 (p0) REVERT: E 151 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8445 (tpp) REVERT: E 159 MET cc_start: 0.8499 (tpt) cc_final: 0.7085 (ttp) REVERT: F 9 ASN cc_start: 0.8007 (m-40) cc_final: 0.7761 (m110) REVERT: F 18 ASP cc_start: 0.8707 (t0) cc_final: 0.8397 (p0) REVERT: F 75 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8292 (tpt-90) REVERT: F 131 TYR cc_start: 0.7956 (p90) cc_final: 0.7044 (p90) REVERT: F 156 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8585 (t0) outliers start: 67 outliers final: 49 residues processed: 313 average time/residue: 0.0927 time to fit residues: 43.4006 Evaluate side-chains 315 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088340 restraints weight = 35466.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090435 restraints weight = 16815.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091757 restraints weight = 9566.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092642 restraints weight = 6158.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093152 restraints weight = 4393.117| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12838 Z= 0.154 Angle : 0.615 10.002 17475 Z= 0.322 Chirality : 0.045 0.219 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.533 19.498 1777 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 5.42 % Allowed : 29.47 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.21), residues: 1604 helix: 1.20 (0.30), residues: 285 sheet: -1.19 (0.26), residues: 406 loop : -1.71 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.021 0.002 TYR C 101 PHE 0.021 0.002 PHE B 110 TRP 0.019 0.001 TRP F 37 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00352 (12836) covalent geometry : angle 0.61392 (17471) SS BOND : bond 0.00256 ( 2) SS BOND : angle 2.90423 ( 4) hydrogen bonds : bond 0.03926 ( 429) hydrogen bonds : angle 5.47386 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: A 54 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 199 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8773 (t) REVERT: A 487 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: A 492 GLU cc_start: 0.7653 (tp30) cc_final: 0.6956 (mt-10) REVERT: A 503 ASP cc_start: 0.8172 (t70) cc_final: 0.7850 (t0) REVERT: A 670 MET cc_start: 0.7478 (mtm) cc_final: 0.7267 (mtm) REVERT: B 20 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.8985 (m) REVERT: B 21 PHE cc_start: 0.9068 (m-80) cc_final: 0.8812 (m-80) REVERT: B 35 VAL cc_start: 0.9014 (t) cc_final: 0.8729 (p) REVERT: B 67 THR cc_start: 0.8630 (m) cc_final: 0.8211 (t) REVERT: B 87 ILE cc_start: 0.9089 (tp) cc_final: 0.8839 (tp) REVERT: B 89 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7491 (mm) REVERT: B 92 GLU cc_start: 0.7410 (tp30) cc_final: 0.6959 (tp30) REVERT: B 98 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8040 (mm-40) REVERT: B 107 GLU cc_start: 0.7965 (tp30) cc_final: 0.7487 (tp30) REVERT: B 110 PHE cc_start: 0.8123 (t80) cc_final: 0.7905 (t80) REVERT: B 120 GLN cc_start: 0.8132 (mt0) cc_final: 0.7470 (mt0) REVERT: C 6 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (t0) REVERT: C 9 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7625 (ttp80) REVERT: C 11 GLN cc_start: 0.7668 (tp40) cc_final: 0.7329 (mp10) REVERT: C 91 GLN cc_start: 0.7790 (tt0) cc_final: 0.7541 (pt0) REVERT: C 101 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: C 104 GLU cc_start: 0.7948 (pm20) cc_final: 0.7663 (mp0) REVERT: C 112 ARG cc_start: 0.8924 (mmt180) cc_final: 0.8614 (mmt180) REVERT: E 79 ASP cc_start: 0.7865 (p0) cc_final: 0.7512 (p0) REVERT: E 137 ASP cc_start: 0.8459 (t0) cc_final: 0.8252 (t0) REVERT: E 144 ASP cc_start: 0.8849 (p0) cc_final: 0.8439 (p0) REVERT: E 151 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8318 (tpp) REVERT: E 159 MET cc_start: 0.8443 (tpt) cc_final: 0.7209 (ttp) REVERT: E 161 MET cc_start: 0.8696 (ppp) cc_final: 0.8274 (tmm) REVERT: F 9 ASN cc_start: 0.8031 (m-40) cc_final: 0.7762 (m110) REVERT: F 18 ASP cc_start: 0.8683 (t0) cc_final: 0.8392 (p0) REVERT: F 75 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8299 (tpt-90) REVERT: F 131 TYR cc_start: 0.7875 (p90) cc_final: 0.6990 (p90) REVERT: F 156 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8532 (t0) outliers start: 73 outliers final: 54 residues processed: 317 average time/residue: 0.1043 time to fit residues: 49.1023 Evaluate side-chains 322 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 114 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088354 restraints weight = 35853.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090464 restraints weight = 17000.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091789 restraints weight = 9644.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092668 restraints weight = 6213.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093246 restraints weight = 4432.524| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12838 Z= 0.161 Angle : 0.626 10.677 17475 Z= 0.326 Chirality : 0.046 0.256 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.537 19.235 1777 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.90 % Allowed : 29.62 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.21), residues: 1604 helix: 1.02 (0.30), residues: 285 sheet: -1.22 (0.26), residues: 409 loop : -1.68 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.025 0.002 TYR C 53 PHE 0.023 0.002 PHE F 53 TRP 0.010 0.001 TRP A 216 HIS 0.004 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00368 (12836) covalent geometry : angle 0.62218 (17471) SS BOND : bond 0.00741 ( 2) SS BOND : angle 4.35159 ( 4) hydrogen bonds : bond 0.03975 ( 429) hydrogen bonds : angle 5.50977 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: A 54 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 199 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8752 (t) REVERT: A 487 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: A 492 GLU cc_start: 0.7658 (tp30) cc_final: 0.6961 (mt-10) REVERT: A 503 ASP cc_start: 0.8177 (t70) cc_final: 0.7859 (t0) REVERT: A 670 MET cc_start: 0.7488 (mtm) cc_final: 0.7281 (mtm) REVERT: B 20 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9015 (m) REVERT: B 35 VAL cc_start: 0.9011 (t) cc_final: 0.8725 (p) REVERT: B 67 THR cc_start: 0.8440 (m) cc_final: 0.8032 (t) REVERT: B 87 ILE cc_start: 0.9091 (tp) cc_final: 0.8828 (tp) REVERT: B 89 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7503 (mm) REVERT: B 92 GLU cc_start: 0.7412 (tp30) cc_final: 0.6913 (tp30) REVERT: B 98 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8056 (mm-40) REVERT: B 107 GLU cc_start: 0.7952 (tp30) cc_final: 0.7455 (tp30) REVERT: B 120 GLN cc_start: 0.8133 (mt0) cc_final: 0.7470 (mt0) REVERT: C 6 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7789 (t0) REVERT: C 9 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7601 (ttp80) REVERT: C 11 GLN cc_start: 0.7685 (tp40) cc_final: 0.7346 (mp10) REVERT: C 91 GLN cc_start: 0.7775 (tt0) cc_final: 0.7540 (pt0) REVERT: C 101 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: C 112 ARG cc_start: 0.8876 (mmt180) cc_final: 0.8601 (mmt180) REVERT: E 25 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7435 (t) REVERT: E 79 ASP cc_start: 0.7861 (p0) cc_final: 0.7519 (p0) REVERT: E 92 TYR cc_start: 0.8135 (t80) cc_final: 0.7577 (m-80) REVERT: E 144 ASP cc_start: 0.8842 (p0) cc_final: 0.8451 (p0) REVERT: E 151 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: E 159 MET cc_start: 0.8398 (tpt) cc_final: 0.7267 (ttp) REVERT: E 161 MET cc_start: 0.8695 (ppp) cc_final: 0.8378 (tmm) REVERT: F 5 VAL cc_start: 0.9006 (p) cc_final: 0.8764 (p) REVERT: F 9 ASN cc_start: 0.8079 (m-40) cc_final: 0.7773 (m110) REVERT: F 14 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8512 (t0) REVERT: F 18 ASP cc_start: 0.8620 (t0) cc_final: 0.8340 (p0) REVERT: F 75 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8388 (tpt-90) REVERT: F 131 TYR cc_start: 0.7873 (p90) cc_final: 0.6979 (p90) REVERT: F 156 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8229 (t0) outliers start: 66 outliers final: 54 residues processed: 309 average time/residue: 0.1010 time to fit residues: 46.4051 Evaluate side-chains 317 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 251 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 156 ASN Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN F 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086135 restraints weight = 35795.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088194 restraints weight = 17164.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089506 restraints weight = 9835.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090374 restraints weight = 6376.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090937 restraints weight = 4570.503| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12838 Z= 0.214 Angle : 0.663 11.025 17475 Z= 0.347 Chirality : 0.047 0.290 1940 Planarity : 0.004 0.042 2322 Dihedral : 4.704 19.172 1777 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 4.97 % Allowed : 29.70 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.21), residues: 1604 helix: 0.89 (0.30), residues: 286 sheet: -1.27 (0.26), residues: 413 loop : -1.72 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 10 TYR 0.025 0.002 TYR E 92 PHE 0.022 0.002 PHE F 53 TRP 0.012 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 Details of bonding type rmsd covalent geometry : bond 0.00486 (12836) covalent geometry : angle 0.65771 (17471) SS BOND : bond 0.01007 ( 2) SS BOND : angle 5.33207 ( 4) hydrogen bonds : bond 0.04318 ( 429) hydrogen bonds : angle 5.66369 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.56 seconds wall clock time: 35 minutes 7.03 seconds (2107.03 seconds total)