Starting phenix.real_space_refine on Wed Feb 4 20:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzw_47340/02_2026/9dzw_47340.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 4181 2.51 5 N 1002 2.21 5 O 1020 1.98 5 H 6550 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12765 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2132 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2126 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.25, per 1000 atoms: 0.18 Number of scatterers: 12765 At special positions: 0 Unit cell: (81.48, 84, 70.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 1020 8.00 N 1002 7.00 C 4181 6.00 H 6550 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 295.7 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 96.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Processing helix chain 'A' and resid 34 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.624A pdb=" N ALA A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 141 removed outlier: 4.153A pdb=" N MET A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 32 removed outlier: 4.580A pdb=" N LEU B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 66 removed outlier: 3.509A pdb=" N ALA B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.662A pdb=" N ALA B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 107 through 138 removed outlier: 3.926A pdb=" N TYR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 32 removed outlier: 4.020A pdb=" N ARG C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 66 removed outlier: 3.512A pdb=" N LEU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 102 removed outlier: 3.856A pdb=" N ALA C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 107 through 140 removed outlier: 3.541A pdb=" N TYR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 134 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 32 Processing helix chain 'D' and resid 34 through 66 Processing helix chain 'D' and resid 69 through 102 removed outlier: 3.864A pdb=" N ALA D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 107 through 141 removed outlier: 3.825A pdb=" N TYR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 32 Processing helix chain 'E' and resid 34 through 66 Processing helix chain 'E' and resid 69 through 102 Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 137 removed outlier: 3.813A pdb=" N TYR E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU E 134 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ALA E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 32 removed outlier: 3.934A pdb=" N ARG F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 67 removed outlier: 3.869A pdb=" N GLY F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 102 removed outlier: 3.522A pdb=" N ALA F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 107 through 141 removed outlier: 3.683A pdb=" N TYR F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 126 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU F 134 " --> pdb=" O TRP F 130 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 6550 1.12 - 1.29: 969 1.29 - 1.47: 2135 1.47 - 1.64: 3201 1.64 - 1.82: 24 Bond restraints: 12879 Sorted by residual: bond pdb=" N VAL E 23 " pdb=" H VAL E 23 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE1 PHE D 40 " pdb=" HE1 PHE D 40 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ALA F 11 " pdb=" H ALA F 11 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N LEU F 77 " pdb=" H LEU F 77 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD1 PHE E 40 " pdb=" HD1 PHE E 40 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 12874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.91: 23287 6.91 - 13.81: 188 13.81 - 20.72: 0 20.72 - 27.63: 1 27.63 - 34.54: 8 Bond angle restraints: 23484 Sorted by residual: angle pdb=" C TYR D 30 " pdb=" CA TYR D 30 " pdb=" HA TYR D 30 " ideal model delta sigma weight residual 109.00 74.46 34.54 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C ARG B 9 " pdb=" CA ARG B 9 " pdb=" HA ARG B 9 " ideal model delta sigma weight residual 109.00 74.51 34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C LEU D 31 " pdb=" CA LEU D 31 " pdb=" HA LEU D 31 " ideal model delta sigma weight residual 109.00 74.99 34.01 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N TYR D 30 " pdb=" CA TYR D 30 " pdb=" HA TYR D 30 " ideal model delta sigma weight residual 110.00 76.43 33.57 3.00e+00 1.11e-01 1.25e+02 angle pdb=" N LEU D 31 " pdb=" CA LEU D 31 " pdb=" HA LEU D 31 " ideal model delta sigma weight residual 110.00 76.89 33.11 3.00e+00 1.11e-01 1.22e+02 ... (remaining 23479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 5372 16.00 - 32.01: 312 32.01 - 48.01: 99 48.01 - 64.01: 139 64.01 - 80.02: 21 Dihedral angle restraints: 5943 sinusoidal: 3111 harmonic: 2832 Sorted by residual: dihedral pdb=" C TYR D 30 " pdb=" N TYR D 30 " pdb=" CA TYR D 30 " pdb=" CB TYR D 30 " ideal model delta harmonic sigma weight residual -122.60 -138.13 15.53 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" C ARG B 9 " pdb=" N ARG B 9 " pdb=" CA ARG B 9 " pdb=" CB ARG B 9 " ideal model delta harmonic sigma weight residual -122.60 -137.69 15.09 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" CA LEU A 139 " pdb=" C LEU A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 5940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 968 0.127 - 0.254: 146 0.254 - 0.382: 9 0.382 - 0.509: 2 0.509 - 0.636: 2 Chirality restraints: 1127 Sorted by residual: chirality pdb=" CA TYR D 30 " pdb=" N TYR D 30 " pdb=" C TYR D 30 " pdb=" CB TYR D 30 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA ARG B 9 " pdb=" N ARG B 9 " pdb=" C ARG B 9 " pdb=" CB ARG B 9 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA LEU D 31 " pdb=" N LEU D 31 " pdb=" C LEU D 31 " pdb=" CB LEU D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 1124 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 58 " 0.149 2.00e-02 2.50e+03 6.86e-02 1.88e+02 pdb=" CG TRP D 58 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 58 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 58 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP D 58 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP D 58 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 58 " -0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 58 " 0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 58 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP D 58 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP D 58 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP D 58 " -0.136 2.00e-02 2.50e+03 pdb=" HE3 TRP D 58 " -0.076 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 58 " 0.094 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 58 " -0.060 2.00e-02 2.50e+03 pdb=" HH2 TRP D 58 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 58 " 0.186 2.00e-02 2.50e+03 6.76e-02 1.83e+02 pdb=" CG TRP F 58 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP F 58 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP F 58 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 58 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP F 58 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 58 " -0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 58 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 58 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP F 58 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP F 58 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP F 58 " -0.077 2.00e-02 2.50e+03 pdb=" HE3 TRP F 58 " -0.115 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 58 " 0.050 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 58 " -0.038 2.00e-02 2.50e+03 pdb=" HH2 TRP F 58 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 58 " -0.099 2.00e-02 2.50e+03 5.68e-02 1.29e+02 pdb=" CG TRP C 58 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 58 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 58 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP C 58 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 58 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP C 58 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 58 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 58 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP C 58 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 TRP C 58 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP C 58 " 0.130 2.00e-02 2.50e+03 pdb=" HE3 TRP C 58 " 0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 58 " -0.061 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 58 " 0.053 2.00e-02 2.50e+03 pdb=" HH2 TRP C 58 " -0.042 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 898 2.26 - 2.85: 26926 2.85 - 3.43: 36904 3.43 - 4.02: 46779 4.02 - 4.60: 68169 Nonbonded interactions: 179676 Sorted by model distance: nonbonded pdb=" O LEU C 79 " pdb=" HG1 THR C 83 " model vdw 1.677 2.450 nonbonded pdb=" O LEU B 79 " pdb=" HG1 THR B 83 " model vdw 1.684 2.450 nonbonded pdb=" H LEU D 31 " pdb=" HA LEU D 31 " model vdw 1.695 1.816 nonbonded pdb=" O ALA E 90 " pdb=" HG1 THR E 94 " model vdw 1.697 2.450 nonbonded pdb=" O ALA C 90 " pdb=" HG1 THR C 94 " model vdw 1.701 2.450 ... (remaining 179671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 52 through 73 or (resid 7 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name H or \ name HA or name HB2 or name HB3)) or resid 75 or (resid 76 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 77 through 141 \ )) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 77 through 141)) selection = (chain 'C' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB or name CG or name H or name HA or name HB2 or name HB3)) \ or resid 75 or (resid 76 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 77 through 141)) selection = (chain 'D' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB or name CG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 141)) selection = (chain 'E' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB or name CG or name H or name HA or name HB2 or name HB3)) \ or resid 75 or (resid 76 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 77 through 141)) selection = (chain 'F' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB or name CG or name H or name HA or name HB2 or name HB3)) \ or resid 75 or (resid 76 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 77 through 141)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 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 : 0.012 0.046 6329 Z= 0.767 Angle : 1.795 9.780 8674 Z= 1.205 Chirality : 0.093 0.636 1127 Planarity : 0.015 0.111 1044 Dihedral : 13.056 74.959 2106 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.13 % Allowed : 7.10 % Favored : 90.76 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.22), residues: 834 helix: -1.88 (0.14), residues: 780 sheet: None (None), residues: 0 loop : -2.00 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 38 TYR 0.116 0.023 TYR D 106 PHE 0.061 0.013 PHE C 40 TRP 0.112 0.021 TRP F 58 HIS 0.006 0.003 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.01240 ( 6329) covalent geometry : angle 1.79489 ( 8674) hydrogen bonds : bond 0.15035 ( 646) hydrogen bonds : angle 7.30464 ( 1923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 LEU cc_start: 0.3894 (OUTLIER) cc_final: 0.2832 (mt) REVERT: E 132 LEU cc_start: 0.5385 (pp) cc_final: 0.5103 (pp) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.1683 time to fit residues: 27.5846 Evaluate side-chains 108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain F residue 13 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.201032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.186190 restraints weight = 32130.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.192907 restraints weight = 15223.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.196593 restraints weight = 7719.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.198612 restraints weight = 4079.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.199668 restraints weight = 2221.324| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6329 Z= 0.230 Angle : 0.701 7.997 8674 Z= 0.368 Chirality : 0.042 0.496 1127 Planarity : 0.005 0.037 1044 Dihedral : 7.701 77.242 925 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.55 % Allowed : 14.39 % Favored : 82.06 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 834 helix: -0.44 (0.16), residues: 780 sheet: None (None), residues: 0 loop : -1.68 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 9 TYR 0.027 0.002 TYR D 30 PHE 0.012 0.002 PHE F 114 TRP 0.014 0.001 TRP E 130 HIS 0.007 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6329) covalent geometry : angle 0.70110 ( 8674) hydrogen bonds : bond 0.06497 ( 646) hydrogen bonds : angle 5.27814 ( 1923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 LEU cc_start: 0.4741 (pp) cc_final: 0.4473 (pp) REVERT: F 28 LEU cc_start: 0.7154 (mt) cc_final: 0.6904 (mm) REVERT: F 136 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5201 (tt) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1781 time to fit residues: 28.1207 Evaluate side-chains 119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.198662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.184686 restraints weight = 32172.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.191041 restraints weight = 15159.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.194439 restraints weight = 7684.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.196396 restraints weight = 4084.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.197401 restraints weight = 2214.080| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6329 Z= 0.209 Angle : 0.636 8.288 8674 Z= 0.341 Chirality : 0.039 0.477 1127 Planarity : 0.004 0.037 1044 Dihedral : 6.901 79.047 919 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.09 % Allowed : 14.74 % Favored : 81.17 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 834 helix: -0.02 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -0.93 (0.93), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 4 TYR 0.023 0.002 TYR D 30 PHE 0.018 0.002 PHE A 95 TRP 0.010 0.001 TRP F 58 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6329) covalent geometry : angle 0.63581 ( 8674) hydrogen bonds : bond 0.05872 ( 646) hydrogen bonds : angle 4.97133 ( 1923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LEU cc_start: 0.7003 (tp) cc_final: 0.6775 (tp) REVERT: E 56 LEU cc_start: 0.2236 (OUTLIER) cc_final: 0.1677 (mt) REVERT: E 132 LEU cc_start: 0.4308 (pp) cc_final: 0.4091 (pp) REVERT: F 136 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.5068 (tt) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.1616 time to fit residues: 26.2598 Evaluate side-chains 122 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.199440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.184539 restraints weight = 31724.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.190996 restraints weight = 15137.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.194647 restraints weight = 7823.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.196751 restraints weight = 4278.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.197854 restraints weight = 2409.071| |-----------------------------------------------------------------------------| r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6329 Z= 0.215 Angle : 0.629 8.079 8674 Z= 0.334 Chirality : 0.039 0.473 1127 Planarity : 0.004 0.039 1044 Dihedral : 6.632 78.844 917 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.97 % Allowed : 14.56 % Favored : 80.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 834 helix: 0.26 (0.17), residues: 774 sheet: None (None), residues: 0 loop : 0.17 (0.95), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 38 TYR 0.022 0.001 TYR D 30 PHE 0.018 0.002 PHE A 95 TRP 0.009 0.001 TRP F 58 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6329) covalent geometry : angle 0.62852 ( 8674) hydrogen bonds : bond 0.05588 ( 646) hydrogen bonds : angle 4.87936 ( 1923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 LEU cc_start: 0.2255 (OUTLIER) cc_final: 0.1663 (mt) REVERT: E 128 LEU cc_start: 0.4709 (OUTLIER) cc_final: 0.4395 (mt) REVERT: E 132 LEU cc_start: 0.4356 (pp) cc_final: 0.4100 (pp) REVERT: F 111 LEU cc_start: 0.7087 (tp) cc_final: 0.6876 (tp) REVERT: F 119 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5936 (tt) outliers start: 28 outliers final: 21 residues processed: 121 average time/residue: 0.1573 time to fit residues: 26.1106 Evaluate side-chains 127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.200217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.185379 restraints weight = 32121.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.191898 restraints weight = 15460.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.195541 restraints weight = 8029.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.197610 restraints weight = 4382.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.198711 restraints weight = 2463.648| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5294 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6329 Z= 0.182 Angle : 0.604 7.623 8674 Z= 0.315 Chirality : 0.038 0.468 1127 Planarity : 0.004 0.038 1044 Dihedral : 6.421 79.652 917 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.97 % Allowed : 15.10 % Favored : 79.93 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 834 helix: 0.62 (0.18), residues: 774 sheet: None (None), residues: 0 loop : 0.18 (0.96), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 38 TYR 0.019 0.001 TYR D 30 PHE 0.014 0.002 PHE A 95 TRP 0.007 0.001 TRP F 58 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6329) covalent geometry : angle 0.60424 ( 8674) hydrogen bonds : bond 0.05087 ( 646) hydrogen bonds : angle 4.64238 ( 1923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.4704 (OUTLIER) cc_final: 0.4014 (tpt) REVERT: D 83 THR cc_start: 0.6347 (t) cc_final: 0.5966 (p) REVERT: E 56 LEU cc_start: 0.2060 (OUTLIER) cc_final: 0.1488 (mt) REVERT: F 136 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4873 (tt) outliers start: 28 outliers final: 21 residues processed: 127 average time/residue: 0.1626 time to fit residues: 28.0233 Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 66 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.198772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.184678 restraints weight = 33315.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.190800 restraints weight = 15970.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.194378 restraints weight = 8255.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.196387 restraints weight = 4459.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.197391 restraints weight = 2455.156| |-----------------------------------------------------------------------------| r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6329 Z= 0.193 Angle : 0.619 7.735 8674 Z= 0.320 Chirality : 0.039 0.469 1127 Planarity : 0.004 0.042 1044 Dihedral : 6.381 79.587 917 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.80 % Allowed : 16.87 % Favored : 78.33 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 834 helix: 0.73 (0.18), residues: 774 sheet: None (None), residues: 0 loop : 0.17 (0.97), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 38 TYR 0.019 0.001 TYR D 30 PHE 0.011 0.001 PHE F 114 TRP 0.007 0.001 TRP F 58 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6329) covalent geometry : angle 0.61947 ( 8674) hydrogen bonds : bond 0.05084 ( 646) hydrogen bonds : angle 4.61790 ( 1923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.5361 (ttt180) cc_final: 0.5128 (ttt180) REVERT: C 91 MET cc_start: 0.4697 (OUTLIER) cc_final: 0.3974 (tpt) REVERT: D 83 THR cc_start: 0.6411 (t) cc_final: 0.5986 (p) REVERT: E 56 LEU cc_start: 0.2080 (OUTLIER) cc_final: 0.1502 (mt) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.1688 time to fit residues: 28.9362 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.198370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.184325 restraints weight = 33772.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.190552 restraints weight = 15920.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.194083 restraints weight = 8071.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.196044 restraints weight = 4308.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.197023 restraints weight = 2356.254| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6329 Z= 0.203 Angle : 0.633 8.230 8674 Z= 0.327 Chirality : 0.038 0.468 1127 Planarity : 0.004 0.043 1044 Dihedral : 6.368 79.610 917 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.44 % Allowed : 17.41 % Favored : 78.15 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.28), residues: 834 helix: 0.72 (0.18), residues: 774 sheet: None (None), residues: 0 loop : 0.08 (0.97), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 38 TYR 0.019 0.001 TYR D 30 PHE 0.011 0.002 PHE F 114 TRP 0.008 0.001 TRP F 58 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6329) covalent geometry : angle 0.63253 ( 8674) hydrogen bonds : bond 0.05117 ( 646) hydrogen bonds : angle 4.63749 ( 1923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.5406 (ttt180) cc_final: 0.5172 (ttt180) REVERT: C 91 MET cc_start: 0.4669 (OUTLIER) cc_final: 0.3935 (tpt) REVERT: D 83 THR cc_start: 0.6428 (t) cc_final: 0.5993 (p) REVERT: E 56 LEU cc_start: 0.2089 (OUTLIER) cc_final: 0.1515 (mt) outliers start: 25 outliers final: 21 residues processed: 123 average time/residue: 0.1639 time to fit residues: 27.5140 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.199330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.185436 restraints weight = 33127.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.191529 restraints weight = 15858.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.195060 restraints weight = 8177.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.197003 restraints weight = 4400.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.198031 restraints weight = 2425.647| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6329 Z= 0.169 Angle : 0.606 8.834 8674 Z= 0.308 Chirality : 0.038 0.461 1127 Planarity : 0.004 0.045 1044 Dihedral : 6.076 79.750 915 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.09 % Allowed : 17.41 % Favored : 78.51 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.28), residues: 834 helix: 0.98 (0.18), residues: 774 sheet: None (None), residues: 0 loop : 0.07 (0.97), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 4 TYR 0.017 0.001 TYR D 30 PHE 0.014 0.002 PHE F 52 TRP 0.007 0.001 TRP F 58 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6329) covalent geometry : angle 0.60583 ( 8674) hydrogen bonds : bond 0.04745 ( 646) hydrogen bonds : angle 4.44010 ( 1923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.5388 (ttt180) cc_final: 0.5148 (ttt180) REVERT: C 91 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.3987 (tpt) REVERT: D 83 THR cc_start: 0.6336 (t) cc_final: 0.5900 (p) REVERT: E 56 LEU cc_start: 0.1999 (OUTLIER) cc_final: 0.1420 (mt) outliers start: 23 outliers final: 20 residues processed: 123 average time/residue: 0.1854 time to fit residues: 30.7520 Evaluate side-chains 128 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.198134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.184445 restraints weight = 33540.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.190346 restraints weight = 15838.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.193862 restraints weight = 8144.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.195779 restraints weight = 4354.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.196804 restraints weight = 2400.108| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6329 Z= 0.220 Angle : 0.654 7.305 8674 Z= 0.339 Chirality : 0.039 0.467 1127 Planarity : 0.004 0.045 1044 Dihedral : 6.223 80.028 915 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.26 % Allowed : 18.29 % Favored : 77.44 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.28), residues: 834 helix: 0.69 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -0.01 (0.96), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 4 TYR 0.019 0.001 TYR D 30 PHE 0.011 0.002 PHE F 114 TRP 0.008 0.001 TRP F 58 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6329) covalent geometry : angle 0.65396 ( 8674) hydrogen bonds : bond 0.05155 ( 646) hydrogen bonds : angle 4.69353 ( 1923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.3857 (tpt) REVERT: D 83 THR cc_start: 0.6416 (t) cc_final: 0.5977 (p) REVERT: E 56 LEU cc_start: 0.1996 (OUTLIER) cc_final: 0.1412 (mt) outliers start: 24 outliers final: 22 residues processed: 123 average time/residue: 0.1695 time to fit residues: 28.4741 Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.198866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.185016 restraints weight = 33308.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.191091 restraints weight = 15868.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.194568 restraints weight = 8114.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.196513 restraints weight = 4364.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.197517 restraints weight = 2401.655| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6329 Z= 0.180 Angle : 0.618 7.840 8674 Z= 0.314 Chirality : 0.039 0.464 1127 Planarity : 0.004 0.049 1044 Dihedral : 6.084 80.216 915 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.09 % Allowed : 18.65 % Favored : 77.26 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.28), residues: 834 helix: 0.93 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -0.09 (0.94), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 4 TYR 0.018 0.001 TYR D 30 PHE 0.011 0.002 PHE F 114 TRP 0.008 0.001 TRP F 58 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6329) covalent geometry : angle 0.61809 ( 8674) hydrogen bonds : bond 0.04760 ( 646) hydrogen bonds : angle 4.48913 ( 1923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ALA 76 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 65 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.3927 (tpt) REVERT: D 83 THR cc_start: 0.6386 (t) cc_final: 0.5930 (p) REVERT: E 56 LEU cc_start: 0.1919 (OUTLIER) cc_final: 0.1332 (mt) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 0.1702 time to fit residues: 28.5749 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 13 TRP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.198312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.184595 restraints weight = 33345.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.190602 restraints weight = 15816.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.194050 restraints weight = 8088.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.195974 restraints weight = 4350.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.196945 restraints weight = 2383.477| |-----------------------------------------------------------------------------| r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6329 Z= 0.218 Angle : 0.655 7.145 8674 Z= 0.339 Chirality : 0.039 0.471 1127 Planarity : 0.004 0.050 1044 Dihedral : 6.171 79.825 915 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.09 % Allowed : 19.01 % Favored : 76.91 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 834 helix: 0.76 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -0.20 (0.93), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 38 TYR 0.020 0.001 TYR D 30 PHE 0.011 0.002 PHE F 114 TRP 0.008 0.001 TRP F 58 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6329) covalent geometry : angle 0.65535 ( 8674) hydrogen bonds : bond 0.05095 ( 646) hydrogen bonds : angle 4.67045 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.54 seconds wall clock time: 35 minutes 39.61 seconds (2139.61 seconds total)