Starting phenix.real_space_refine on Thu May 15 01:53:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ck1_16689/05_2025/8ck1_16689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ck1_16689/05_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_16689/05_2025/8ck1_16689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ck1_16689/05_2025/8ck1_16689.map" model { file = "/net/cci-nas-00/data/ceres_data/8ck1_16689/05_2025/8ck1_16689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ck1_16689/05_2025/8ck1_16689.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.88, per 1000 atoms: 0.63 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.76 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: 4.72 Time building geometry restraints manager: 3.61 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.340 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), 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 TRP 0.025 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 PHE 0.015 0.002 PHE F 53 TYR 0.037 0.002 TYR F 104 ARG 0.004 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.21862 ( 429) hydrogen bonds : angle 8.74618 ( 1089) SS BOND : bond 0.00427 ( 2) SS BOND : angle 3.95646 ( 4) covalent geometry : bond 0.00422 (12836) covalent geometry : angle 0.74944 (17471) *********************** 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 : 1.443 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: 0.7338 (tm-30) REVERT: D 68 PHE cc_start: 0.5675 (t80) cc_final: 0.5286 (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: 0.7535 (mp0) REVERT: C 112 ARG cc_start: 0.8921 (mmt180) cc_final: 0.8533 (mmt180) REVERT: E 27 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7258 (mtpt) REVERT: E 79 ASP cc_start: 0.7581 (p0) cc_final: 0.7338 (p0) REVERT: E 94 ASP cc_start: 0.7228 (t70) cc_final: 0.6789 (t70) REVERT: E 144 ASP cc_start: 0.8980 (p0) cc_final: 0.8724 (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: 0.2454 time to fit residues: 114.6520 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 : 1.353 ------------------------------------------------------------------------------- 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 133 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 D 6 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086015 restraints weight = 35335.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088138 restraints weight = 16813.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089491 restraints weight = 9599.915| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1515 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= 0.211 Angle : 0.629 8.597 17475 Z= 0.334 Chirality : 0.046 0.193 1940 Planarity : 0.005 0.055 2322 Dihedral : 5.098 50.949 1787 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.60 % Allowed : 25.46 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1604 helix: 0.82 (0.30), residues: 287 sheet: -1.72 (0.25), residues: 432 loop : -1.78 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 37 HIS 0.004 0.001 HIS F 84 PHE 0.015 0.002 PHE D 21 TYR 0.024 0.002 TYR A 482 ARG 0.004 0.001 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 429) hydrogen bonds : angle 6.42202 ( 1089) SS BOND : bond 0.00430 ( 2) SS BOND : angle 2.53899 ( 4) covalent geometry : bond 0.00472 (12836) covalent geometry : angle 0.62794 (17471) *********************** 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 335 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 487 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: A 492 GLU cc_start: 0.8174 (tp30) cc_final: 0.7060 (mt-10) REVERT: D 111 ASP cc_start: 0.8355 (m-30) cc_final: 0.8142 (m-30) REVERT: B 67 THR cc_start: 0.8681 (m) cc_final: 0.8284 (t) REVERT: B 110 PHE cc_start: 0.8089 (t80) cc_final: 0.7836 (t80) REVERT: B 120 GLN cc_start: 0.8573 (mt0) cc_final: 0.8108 (mt0) REVERT: C 81 LEU cc_start: 0.6028 (tp) cc_final: 0.5760 (mm) REVERT: C 98 GLN cc_start: 0.8636 (mp10) cc_final: 0.8391 (mp10) REVERT: C 101 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: C 112 ARG cc_start: 0.8932 (mmt180) cc_final: 0.8441 (mmt180) REVERT: C 119 GLN cc_start: 0.8556 (mt0) cc_final: 0.8072 (mp10) REVERT: E 14 ASN cc_start: 0.9082 (t0) cc_final: 0.8774 (t0) REVERT: E 27 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7667 (mtpt) REVERT: E 79 ASP cc_start: 0.7964 (p0) cc_final: 0.7614 (p0) REVERT: E 94 ASP cc_start: 0.7185 (t0) cc_final: 0.6868 (t70) REVERT: E 144 ASP cc_start: 0.9018 (p0) cc_final: 0.8653 (p0) REVERT: E 151 MET cc_start: 0.9220 (mmm) cc_final: 0.8903 (tpt) REVERT: F 4 LYS cc_start: 0.6220 (tmtt) cc_final: 0.5532 (tptp) REVERT: F 9 ASN cc_start: 0.7944 (m-40) cc_final: 0.7618 (m110) REVERT: F 18 ASP cc_start: 0.8756 (t0) cc_final: 0.8422 (p0) REVERT: F 131 TYR cc_start: 0.7780 (p90) cc_final: 0.7254 (p90) REVERT: F 141 MET cc_start: 0.8787 (pmm) cc_final: 0.8470 (pmm) outliers start: 62 outliers final: 34 residues processed: 310 average time/residue: 0.2752 time to fit residues: 126.5531 Evaluate side-chains 289 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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 47 LEU 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 5 VAL 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 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 71 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.0770 chunk 139 optimal weight: 10.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN 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 F 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086994 restraints weight = 35584.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089151 restraints weight = 16898.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090524 restraints weight = 9654.697| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1923 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= 0.151 Angle : 0.577 9.840 17475 Z= 0.303 Chirality : 0.044 0.203 1940 Planarity : 0.004 0.046 2322 Dihedral : 4.513 20.438 1777 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.49 % Allowed : 27.25 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1604 helix: 1.23 (0.30), residues: 289 sheet: -1.41 (0.26), residues: 405 loop : -1.83 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 37 HIS 0.004 0.001 HIS F 84 PHE 0.013 0.001 PHE F 53 TYR 0.021 0.001 TYR C 101 ARG 0.004 0.000 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 429) hydrogen bonds : angle 5.83390 ( 1089) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.72491 ( 4) covalent geometry : bond 0.00340 (12836) covalent geometry : angle 0.57693 (17471) *********************** 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 317 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: A 487 TRP cc_start: 0.8546 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: A 492 GLU cc_start: 0.8114 (tp30) cc_final: 0.7037 (mt-10) REVERT: A 670 MET cc_start: 0.7618 (mtm) cc_final: 0.7159 (mtm) REVERT: D 62 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 121 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7952 (tm-30) REVERT: B 9 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7992 (ttm-80) REVERT: B 67 THR cc_start: 0.8675 (m) cc_final: 0.8282 (t) REVERT: B 87 ILE cc_start: 0.9156 (tp) cc_final: 0.8921 (tp) REVERT: B 92 GLU cc_start: 0.7597 (tp30) cc_final: 0.7383 (tp30) REVERT: B 98 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7897 (mm-40) REVERT: B 120 GLN cc_start: 0.8303 (mt0) cc_final: 0.7591 (mt0) REVERT: C 98 GLN cc_start: 0.8615 (mp10) cc_final: 0.8361 (mp10) REVERT: C 101 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: C 119 GLN cc_start: 0.8470 (mt0) cc_final: 0.8234 (mp10) REVERT: E 27 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7719 (mtpt) REVERT: E 79 ASP cc_start: 0.7943 (p0) cc_final: 0.7555 (p0) REVERT: E 94 ASP cc_start: 0.7671 (t0) cc_final: 0.7348 (t70) REVERT: E 144 ASP cc_start: 0.8972 (p0) cc_final: 0.8561 (p0) REVERT: E 151 MET cc_start: 0.9244 (mmm) cc_final: 0.8889 (tpt) REVERT: F 3 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8615 (p) REVERT: F 4 LYS cc_start: 0.6039 (tmtt) cc_final: 0.5680 (tptp) REVERT: F 9 ASN cc_start: 0.8014 (m-40) cc_final: 0.7766 (m110) REVERT: F 18 ASP cc_start: 0.8718 (t0) cc_final: 0.8419 (p0) REVERT: F 131 TYR cc_start: 0.7960 (p90) cc_final: 0.7369 (p90) REVERT: F 141 MET cc_start: 0.8826 (pmm) cc_final: 0.8606 (pmm) REVERT: F 156 ASN cc_start: 0.8718 (t0) cc_final: 0.8462 (t0) REVERT: F 159 MET cc_start: 0.8052 (tpp) cc_final: 0.7811 (mmt) outliers start: 47 outliers final: 28 residues processed: 304 average time/residue: 0.2301 time to fit residues: 103.9096 Evaluate side-chains 280 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 72 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 647 VAL Chi-restraints excluded: chain A residue 693 VAL 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 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 3 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 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 3 SER Chi-restraints excluded: chain F residue 36 GLN 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 117 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.0020 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN F 36 GLN ** F 84 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.100377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089387 restraints weight = 34857.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091578 restraints weight = 16507.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092961 restraints weight = 9387.623| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12838 Z= 0.113 Angle : 0.552 10.162 17475 Z= 0.288 Chirality : 0.043 0.209 1940 Planarity : 0.004 0.038 2322 Dihedral : 4.286 19.810 1777 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.56 % Allowed : 27.77 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1604 helix: 1.47 (0.30), residues: 289 sheet: -1.34 (0.26), residues: 405 loop : -1.71 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.004 0.001 HIS F 84 PHE 0.013 0.001 PHE F 53 TYR 0.021 0.001 TYR C 53 ARG 0.004 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 429) hydrogen bonds : angle 5.47904 ( 1089) SS BOND : bond 0.00328 ( 2) SS BOND : angle 1.27528 ( 4) covalent geometry : bond 0.00253 (12836) covalent geometry : angle 0.55178 (17471) *********************** 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 333 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: A 54 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 487 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: A 492 GLU cc_start: 0.7846 (tp30) cc_final: 0.6889 (mt-10) REVERT: A 670 MET cc_start: 0.7648 (mtm) cc_final: 0.7108 (mtm) REVERT: D 62 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7642 (tm-30) REVERT: D 108 ASP cc_start: 0.8018 (t0) cc_final: 0.7777 (t0) REVERT: B 9 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8269 (ttm-80) REVERT: B 67 THR cc_start: 0.8522 (m) cc_final: 0.8163 (t) REVERT: B 87 ILE cc_start: 0.9122 (tp) cc_final: 0.8853 (tp) REVERT: B 92 GLU cc_start: 0.7503 (tp30) cc_final: 0.7183 (tp30) REVERT: B 98 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 107 GLU cc_start: 0.7942 (tp30) cc_final: 0.7734 (tp30) REVERT: B 110 PHE cc_start: 0.8182 (t80) cc_final: 0.7955 (t80) REVERT: B 120 GLN cc_start: 0.8317 (mt0) cc_final: 0.7590 (mt0) REVERT: C 9 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7532 (ttp80) REVERT: C 11 GLN cc_start: 0.7657 (tp40) cc_final: 0.7330 (mp10) REVERT: C 48 ILE cc_start: 0.8934 (mm) cc_final: 0.8690 (mt) REVERT: C 91 GLN cc_start: 0.7711 (tt0) cc_final: 0.7362 (pt0) REVERT: C 101 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: C 112 ARG cc_start: 0.8912 (mmt180) cc_final: 0.8417 (mmt180) REVERT: E 27 LYS cc_start: 0.8402 (mtmm) cc_final: 0.7637 (mtpt) REVERT: E 79 ASP cc_start: 0.7827 (p0) cc_final: 0.7438 (p0) REVERT: E 94 ASP cc_start: 0.7931 (t0) cc_final: 0.7505 (t70) REVERT: E 144 ASP cc_start: 0.8910 (p0) cc_final: 0.8495 (p0) REVERT: E 151 MET cc_start: 0.9142 (mmm) cc_final: 0.8914 (tpp) REVERT: F 4 LYS cc_start: 0.6142 (tmtt) cc_final: 0.5680 (tptp) REVERT: F 18 ASP cc_start: 0.8683 (t0) cc_final: 0.8414 (p0) REVERT: F 32 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7307 (mtt-85) REVERT: F 75 ARG cc_start: 0.8663 (tpp80) cc_final: 0.8265 (tpt-90) REVERT: F 131 TYR cc_start: 0.7913 (p90) cc_final: 0.7281 (p90) REVERT: F 156 ASN cc_start: 0.8741 (t0) cc_final: 0.8473 (t0) outliers start: 48 outliers final: 29 residues processed: 322 average time/residue: 0.2217 time to fit residues: 104.7761 Evaluate side-chains 291 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 165 LEU 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 500 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 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 9 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER 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 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 174 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 79 optimal weight: 0.0270 chunk 135 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086502 restraints weight = 35521.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088642 restraints weight = 16910.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090002 restraints weight = 9671.400| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12838 Z= 0.179 Angle : 0.589 10.190 17475 Z= 0.308 Chirality : 0.044 0.217 1940 Planarity : 0.004 0.039 2322 Dihedral : 4.434 19.679 1777 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.83 % Allowed : 28.06 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1604 helix: 1.45 (0.30), residues: 290 sheet: -1.33 (0.26), residues: 412 loop : -1.74 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS F 84 PHE 0.018 0.002 PHE E 99 TYR 0.021 0.002 TYR C 101 ARG 0.003 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 429) hydrogen bonds : angle 5.52934 ( 1089) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.53931 ( 4) covalent geometry : bond 0.00407 (12836) covalent geometry : angle 0.58845 (17471) *********************** 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 320 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: A 54 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 199 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (t) REVERT: A 212 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8068 (tp30) REVERT: A 343 LEU cc_start: 0.8662 (tp) cc_final: 0.8411 (tp) REVERT: A 487 TRP cc_start: 0.8646 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: A 492 GLU cc_start: 0.7797 (tp30) cc_final: 0.6772 (mt-10) REVERT: D 82 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7832 (p) REVERT: D 108 ASP cc_start: 0.8270 (t0) cc_final: 0.8038 (t0) REVERT: B 9 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8295 (ttm-80) REVERT: B 67 THR cc_start: 0.8567 (m) cc_final: 0.8152 (t) REVERT: B 87 ILE cc_start: 0.9085 (tp) cc_final: 0.8785 (tp) REVERT: B 92 GLU cc_start: 0.7465 (tp30) cc_final: 0.7171 (tp30) REVERT: B 98 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7862 (mm-40) REVERT: B 120 GLN cc_start: 0.8267 (mt0) cc_final: 0.7540 (mt0) REVERT: C 9 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7561 (ttp80) REVERT: C 11 GLN cc_start: 0.7741 (tp40) cc_final: 0.7431 (mp10) REVERT: C 48 ILE cc_start: 0.8952 (mm) cc_final: 0.8704 (mt) REVERT: C 101 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: E 79 ASP cc_start: 0.7942 (p0) cc_final: 0.7592 (p0) REVERT: E 137 ASP cc_start: 0.8405 (t0) cc_final: 0.8127 (t0) REVERT: E 144 ASP cc_start: 0.8941 (p0) cc_final: 0.8579 (p0) REVERT: E 151 MET cc_start: 0.9067 (mmm) cc_final: 0.8865 (tpp) REVERT: E 159 MET cc_start: 0.8604 (tpt) cc_final: 0.7447 (tmm) REVERT: E 205 ILE cc_start: 0.8414 (tp) cc_final: 0.8213 (tp) REVERT: F 3 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 9 ASN cc_start: 0.8005 (m-40) cc_final: 0.7739 (m110) REVERT: F 18 ASP cc_start: 0.8711 (t0) cc_final: 0.8353 (p0) REVERT: F 32 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7261 (mtt-85) REVERT: F 75 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8292 (tpt-90) REVERT: F 131 TYR cc_start: 0.7916 (p90) cc_final: 0.7246 (p90) REVERT: F 168 MET cc_start: 0.9165 (ttp) cc_final: 0.8859 (ttt) outliers start: 65 outliers final: 45 residues processed: 302 average time/residue: 0.2415 time to fit residues: 105.5609 Evaluate side-chains 300 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 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 565 SER 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 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 9 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 5 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 59 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 100 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 137 optimal weight: 0.2980 chunk 59 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN D 98 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN E 156 ASN E 173 GLN F 14 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089384 restraints weight = 35703.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091596 restraints weight = 16914.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092962 restraints weight = 9601.492| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2528 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= 0.116 Angle : 0.559 10.035 17475 Z= 0.291 Chirality : 0.043 0.216 1940 Planarity : 0.004 0.037 2322 Dihedral : 4.234 19.357 1777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.38 % Allowed : 28.36 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1604 helix: 1.48 (0.30), residues: 290 sheet: -1.13 (0.26), residues: 394 loop : -1.65 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 37 HIS 0.003 0.001 HIS F 84 PHE 0.015 0.001 PHE B 21 TYR 0.023 0.001 TYR C 53 ARG 0.003 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 429) hydrogen bonds : angle 5.27176 ( 1089) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.23333 ( 4) covalent geometry : bond 0.00262 (12836) covalent geometry : angle 0.55863 (17471) *********************** 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 336 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: A 54 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 199 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8876 (t) REVERT: A 487 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7205 (m-10) REVERT: A 492 GLU cc_start: 0.7812 (tp30) cc_final: 0.6813 (mt-10) REVERT: A 670 MET cc_start: 0.7598 (mtm) cc_final: 0.6848 (mpp) REVERT: D 23 TYR cc_start: 0.6146 (p90) cc_final: 0.5943 (p90) REVERT: D 108 ASP cc_start: 0.8172 (t0) cc_final: 0.7871 (t0) REVERT: B 67 THR cc_start: 0.8487 (m) cc_final: 0.8068 (t) REVERT: B 87 ILE cc_start: 0.9103 (tp) cc_final: 0.8864 (tp) REVERT: B 92 GLU cc_start: 0.7512 (tp30) cc_final: 0.6976 (tp30) REVERT: B 98 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7897 (mm-40) REVERT: B 104 GLU cc_start: 0.8145 (mp0) cc_final: 0.7928 (mp0) REVERT: B 120 GLN cc_start: 0.8275 (mt0) cc_final: 0.7643 (mt0) REVERT: C 9 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7606 (ttp80) REVERT: C 48 ILE cc_start: 0.8870 (mm) cc_final: 0.8612 (mt) REVERT: C 101 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 112 ARG cc_start: 0.8902 (mmt180) cc_final: 0.8494 (mmt180) REVERT: E 38 TYR cc_start: 0.8476 (t80) cc_final: 0.8187 (t80) REVERT: E 79 ASP cc_start: 0.7834 (p0) cc_final: 0.7469 (p0) REVERT: E 144 ASP cc_start: 0.8890 (p0) cc_final: 0.8465 (p0) REVERT: E 159 MET cc_start: 0.8595 (tpt) cc_final: 0.7447 (tmm) REVERT: E 205 ILE cc_start: 0.8339 (tp) cc_final: 0.8139 (tp) REVERT: F 18 ASP cc_start: 0.8767 (t0) cc_final: 0.8435 (p0) REVERT: F 32 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7296 (mtt-85) REVERT: F 73 LYS cc_start: 0.8397 (ptmm) cc_final: 0.8108 (mtmt) REVERT: F 75 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8329 (tpt-90) REVERT: F 106 GLN cc_start: 0.8627 (mm110) cc_final: 0.8227 (mm-40) REVERT: F 131 TYR cc_start: 0.7932 (p90) cc_final: 0.7204 (p90) REVERT: F 156 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8468 (t0) REVERT: F 168 MET cc_start: 0.9083 (ttp) cc_final: 0.8754 (ttp) outliers start: 59 outliers final: 42 residues processed: 323 average time/residue: 0.2522 time to fit residues: 121.0489 Evaluate side-chains 308 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 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 500 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 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 37 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 ILE 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 82 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 36 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 130 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084786 restraints weight = 35959.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086885 restraints weight = 17231.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088222 restraints weight = 9931.912| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12838 Z= 0.277 Angle : 0.682 9.906 17475 Z= 0.359 Chirality : 0.047 0.217 1940 Planarity : 0.005 0.042 2322 Dihedral : 4.822 19.886 1777 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 5.79 % Allowed : 27.84 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1604 helix: 1.05 (0.29), residues: 292 sheet: -1.42 (0.26), residues: 403 loop : -1.85 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 408 HIS 0.007 0.001 HIS F 84 PHE 0.017 0.002 PHE B 110 TYR 0.022 0.002 TYR C 101 ARG 0.005 0.001 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 429) hydrogen bonds : angle 5.74077 ( 1089) SS BOND : bond 0.00239 ( 2) SS BOND : angle 2.12728 ( 4) covalent geometry : bond 0.00625 (12836) covalent geometry : angle 0.68108 (17471) *********************** 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 335 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8508 (p) REVERT: A 199 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8783 (t) REVERT: A 212 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: A 487 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: A 492 GLU cc_start: 0.7990 (tp30) cc_final: 0.7026 (mt-10) REVERT: A 670 MET cc_start: 0.7652 (mtm) cc_final: 0.7213 (mpp) REVERT: D 82 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 9 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8135 (ttm-80) REVERT: B 67 THR cc_start: 0.8638 (m) cc_final: 0.8204 (t) REVERT: B 92 GLU cc_start: 0.7441 (tp30) cc_final: 0.7046 (tp30) REVERT: B 95 LEU cc_start: 0.9044 (mt) cc_final: 0.8735 (tp) REVERT: B 98 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7901 (mm-40) REVERT: B 104 GLU cc_start: 0.8097 (mp0) cc_final: 0.7845 (mp0) REVERT: B 120 GLN cc_start: 0.8267 (mt0) cc_final: 0.7484 (mt0) REVERT: C 48 ILE cc_start: 0.9090 (mm) cc_final: 0.8855 (mt) REVERT: C 101 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: E 27 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8004 (mtpp) REVERT: E 79 ASP cc_start: 0.7964 (p0) cc_final: 0.7663 (p0) REVERT: E 144 ASP cc_start: 0.8956 (p0) cc_final: 0.8588 (p0) REVERT: E 159 MET cc_start: 0.8679 (tpt) cc_final: 0.7453 (tmm) REVERT: F 18 ASP cc_start: 0.8829 (t0) cc_final: 0.8404 (p0) REVERT: F 28 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7261 (m) REVERT: F 30 GLU cc_start: 0.8415 (mp0) cc_final: 0.8163 (mp0) REVERT: F 32 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7349 (mtt-85) REVERT: F 75 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8217 (tpt-90) REVERT: F 106 GLN cc_start: 0.8618 (mm110) cc_final: 0.8134 (mm-40) REVERT: F 131 TYR cc_start: 0.7948 (p90) cc_final: 0.7047 (p90) REVERT: F 156 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8611 (t0) outliers start: 78 outliers final: 58 residues processed: 312 average time/residue: 0.2331 time to fit residues: 105.8351 Evaluate side-chains 317 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 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 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 542 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 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 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 82 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL 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 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 82 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 132 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 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 27 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086179 restraints weight = 35802.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088319 restraints weight = 17090.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089686 restraints weight = 9789.919| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12838 Z= 0.214 Angle : 0.656 9.722 17475 Z= 0.344 Chirality : 0.046 0.219 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.761 20.842 1777 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 5.42 % Allowed : 28.51 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1604 helix: 1.08 (0.30), residues: 286 sheet: -1.39 (0.26), residues: 403 loop : -1.81 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 216 HIS 0.005 0.001 HIS F 84 PHE 0.015 0.002 PHE F 53 TYR 0.024 0.002 TYR C 53 ARG 0.003 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 429) hydrogen bonds : angle 5.63512 ( 1089) SS BOND : bond 0.00882 ( 2) SS BOND : angle 4.02354 ( 4) covalent geometry : bond 0.00485 (12836) covalent geometry : angle 0.65334 (17471) *********************** 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 333 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8748 (m-80) REVERT: A 54 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 199 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8791 (t) REVERT: A 212 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: A 487 TRP cc_start: 0.8797 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: A 492 GLU cc_start: 0.7972 (tp30) cc_final: 0.7214 (mt-10) REVERT: A 670 MET cc_start: 0.7579 (mtm) cc_final: 0.7168 (mpp) REVERT: B 67 THR cc_start: 0.8619 (m) cc_final: 0.8179 (t) REVERT: B 92 GLU cc_start: 0.7423 (tp30) cc_final: 0.6976 (tp30) REVERT: B 98 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7884 (mm-40) REVERT: B 104 GLU cc_start: 0.8028 (mp0) cc_final: 0.7774 (mp0) REVERT: B 107 GLU cc_start: 0.7961 (tp30) cc_final: 0.7551 (tp30) REVERT: B 120 GLN cc_start: 0.8246 (mt0) cc_final: 0.7473 (mt0) REVERT: C 9 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7665 (ttp-170) REVERT: C 48 ILE cc_start: 0.9055 (mm) cc_final: 0.8819 (mt) REVERT: C 91 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: C 101 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: C 112 ARG cc_start: 0.8968 (mmt180) cc_final: 0.8533 (mmt180) REVERT: E 27 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8002 (mtpp) REVERT: E 79 ASP cc_start: 0.7975 (p0) cc_final: 0.7660 (p0) REVERT: E 92 TYR cc_start: 0.8352 (t80) cc_final: 0.7609 (m-80) REVERT: E 104 TYR cc_start: 0.7608 (p90) cc_final: 0.7377 (p90) REVERT: E 144 ASP cc_start: 0.8935 (p0) cc_final: 0.8577 (p0) REVERT: E 159 MET cc_start: 0.8679 (tpt) cc_final: 0.7473 (tmm) REVERT: F 18 ASP cc_start: 0.8751 (t0) cc_final: 0.8380 (p0) REVERT: F 28 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7044 (m) REVERT: F 30 GLU cc_start: 0.8396 (mp0) cc_final: 0.8171 (mp0) REVERT: F 32 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7359 (mtt-85) REVERT: F 75 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8332 (tpt-90) REVERT: F 131 TYR cc_start: 0.7937 (p90) cc_final: 0.7028 (p90) REVERT: F 156 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8597 (t0) outliers start: 73 outliers final: 54 residues processed: 314 average time/residue: 0.2346 time to fit residues: 107.6019 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 : 1.550 ------------------------------------------------------------------------------- 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 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 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 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 37 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL 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 E residue 19 ILE 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 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 183 ILE 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 32 ARG Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 132 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 0.0570 chunk 139 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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 6 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087729 restraints weight = 35635.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089865 restraints weight = 16972.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091206 restraints weight = 9687.312| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12838 Z= 0.147 Angle : 0.619 9.710 17475 Z= 0.322 Chirality : 0.045 0.218 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.552 19.838 1777 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.75 % Allowed : 29.03 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1604 helix: 1.14 (0.30), residues: 286 sheet: -1.29 (0.26), residues: 408 loop : -1.73 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.003 0.001 HIS F 84 PHE 0.021 0.001 PHE B 110 TYR 0.023 0.002 TYR C 101 ARG 0.005 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 429) hydrogen bonds : angle 5.46398 ( 1089) SS BOND : bond 0.00322 ( 2) SS BOND : angle 3.44536 ( 4) covalent geometry : bond 0.00336 (12836) covalent geometry : angle 0.61665 (17471) *********************** 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 332 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: A 54 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8452 (p) REVERT: A 199 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 487 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: A 492 GLU cc_start: 0.7927 (tp30) cc_final: 0.6951 (mt-10) REVERT: A 652 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8862 (t) REVERT: A 670 MET cc_start: 0.7583 (mtm) cc_final: 0.7178 (mpp) REVERT: B 9 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8235 (ttm-80) REVERT: B 67 THR cc_start: 0.8559 (m) cc_final: 0.8126 (t) REVERT: B 92 GLU cc_start: 0.7484 (tp30) cc_final: 0.6964 (tp30) REVERT: B 98 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7980 (mm-40) REVERT: B 104 GLU cc_start: 0.8031 (mp0) cc_final: 0.7798 (mp0) REVERT: B 107 GLU cc_start: 0.7852 (tp30) cc_final: 0.7515 (tp30) REVERT: B 120 GLN cc_start: 0.8306 (mt0) cc_final: 0.7560 (mt0) REVERT: C 11 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7723 (mp10) REVERT: C 48 ILE cc_start: 0.8942 (mm) cc_final: 0.8679 (mt) REVERT: C 101 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: C 112 ARG cc_start: 0.8957 (mmt180) cc_final: 0.8494 (mmt180) REVERT: E 27 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7926 (mtpp) REVERT: E 79 ASP cc_start: 0.7930 (p0) cc_final: 0.7585 (p0) REVERT: E 92 TYR cc_start: 0.8323 (t80) cc_final: 0.7550 (m-80) REVERT: E 144 ASP cc_start: 0.8881 (p0) cc_final: 0.8513 (p0) REVERT: E 151 MET cc_start: 0.9198 (mmm) cc_final: 0.8987 (tpp) REVERT: E 159 MET cc_start: 0.8639 (tpt) cc_final: 0.7273 (ttp) REVERT: F 4 LYS cc_start: 0.5354 (tmtt) cc_final: 0.4690 (tptp) REVERT: F 18 ASP cc_start: 0.8717 (t0) cc_final: 0.8406 (p0) REVERT: F 28 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7402 (m) REVERT: F 32 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7285 (mtt-85) REVERT: F 75 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8362 (tpt-90) REVERT: F 131 TYR cc_start: 0.7902 (p90) cc_final: 0.7032 (p90) REVERT: F 156 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8451 (t0) REVERT: F 168 MET cc_start: 0.9294 (ttt) cc_final: 0.8956 (ttp) outliers start: 64 outliers final: 48 residues processed: 314 average time/residue: 0.2308 time to fit residues: 106.2987 Evaluate side-chains 319 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 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 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 6 ASN 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 2 THR Chi-restraints excluded: chain B residue 9 ARG 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 82 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL 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 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 134 ASP 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 32 ARG Chi-restraints excluded: chain F residue 36 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** C 120 GLN ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087173 restraints weight = 35460.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089307 restraints weight = 16936.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090630 restraints weight = 9713.732| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12838 Z= 0.203 Angle : 0.653 9.716 17475 Z= 0.341 Chirality : 0.046 0.215 1940 Planarity : 0.004 0.042 2322 Dihedral : 4.681 20.492 1777 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.53 % Allowed : 29.40 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1604 helix: 0.98 (0.30), residues: 286 sheet: -1.33 (0.26), residues: 408 loop : -1.79 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.005 0.001 HIS F 84 PHE 0.024 0.002 PHE B 110 TYR 0.025 0.002 TYR C 53 ARG 0.005 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 429) hydrogen bonds : angle 5.57253 ( 1089) SS BOND : bond 0.00265 ( 2) SS BOND : angle 3.61464 ( 4) covalent geometry : bond 0.00462 (12836) covalent geometry : angle 0.65057 (17471) ********************** 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 320 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: A 54 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 199 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8785 (t) REVERT: A 487 TRP cc_start: 0.8781 (OUTLIER) cc_final: 0.7486 (m-10) REVERT: A 492 GLU cc_start: 0.7976 (tp30) cc_final: 0.7229 (mt-10) REVERT: A 652 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8856 (t) REVERT: A 670 MET cc_start: 0.7603 (mtm) cc_final: 0.7186 (mpp) REVERT: D 92 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8487 (mm-30) REVERT: B 9 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: B 67 THR cc_start: 0.8591 (m) cc_final: 0.8158 (t) REVERT: B 92 GLU cc_start: 0.7443 (tp30) cc_final: 0.6954 (tp30) REVERT: B 98 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8019 (mm-40) REVERT: B 104 GLU cc_start: 0.8035 (mp0) cc_final: 0.7771 (mp0) REVERT: C 11 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7728 (mp10) REVERT: C 48 ILE cc_start: 0.9052 (mm) cc_final: 0.8805 (mt) REVERT: C 101 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: C 112 ARG cc_start: 0.8962 (mmt180) cc_final: 0.8440 (mmt180) REVERT: E 25 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7356 (t) REVERT: E 27 LYS cc_start: 0.8670 (mtmm) cc_final: 0.7926 (mtpp) REVERT: E 79 ASP cc_start: 0.7963 (p0) cc_final: 0.7633 (p0) REVERT: E 144 ASP cc_start: 0.8908 (p0) cc_final: 0.8554 (p0) REVERT: E 159 MET cc_start: 0.8570 (tpt) cc_final: 0.7086 (ttp) REVERT: F 14 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8560 (t0) REVERT: F 18 ASP cc_start: 0.8722 (t0) cc_final: 0.8385 (p0) REVERT: F 28 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7331 (m) REVERT: F 30 GLU cc_start: 0.8384 (mp0) cc_final: 0.8173 (mp0) REVERT: F 32 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7317 (mtt-85) REVERT: F 75 ARG cc_start: 0.8729 (tpp80) cc_final: 0.8355 (tpt-90) REVERT: F 131 TYR cc_start: 0.7931 (p90) cc_final: 0.7017 (p90) REVERT: F 156 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8565 (t0) outliers start: 61 outliers final: 46 residues processed: 305 average time/residue: 0.2343 time to fit residues: 104.3562 Evaluate side-chains 310 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 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 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 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 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 B residue 9 ARG 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 82 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL 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 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 134 ASP 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 32 ARG Chi-restraints excluded: chain F residue 36 GLN 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 56 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN C 91 GLN C 119 GLN C 120 GLN ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.088797 restraints weight = 35501.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090964 restraints weight = 16937.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092324 restraints weight = 9643.140| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2877 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= 0.145 Angle : 0.622 9.995 17475 Z= 0.325 Chirality : 0.045 0.215 1940 Planarity : 0.004 0.043 2322 Dihedral : 4.538 19.617 1777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.45 % Allowed : 29.84 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1604 helix: 1.04 (0.30), residues: 285 sheet: -1.16 (0.26), residues: 406 loop : -1.73 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.003 0.001 HIS F 84 PHE 0.022 0.002 PHE B 110 TYR 0.022 0.002 TYR C 101 ARG 0.005 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 429) hydrogen bonds : angle 5.45562 ( 1089) SS BOND : bond 0.00206 ( 2) SS BOND : angle 2.89192 ( 4) covalent geometry : bond 0.00332 (12836) covalent geometry : angle 0.62080 (17471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.38 seconds wall clock time: 71 minutes 32.00 seconds (4292.00 seconds total)