Starting phenix.real_space_refine on Sat Aug 23 09:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2025/8ua7_42053.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 P 259 5.49 5 S 22 5.16 5 C 6251 2.51 5 N 2081 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11263 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 633 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 754 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 755 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 633 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "G" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 754 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 755 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "I" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2676 Classifications: {'DNA': 130} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2651 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Time building chain proxies: 3.15, per 1000 atoms: 0.28 Number of scatterers: 11263 At special positions: 0 Unit cell: (88.27, 117.37, 129.01, 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 22 16.00 P 259 15.00 O 2650 8.00 N 2081 7.00 C 6251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 254.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 66.2% alpha, 0.0% beta 89 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.522A pdb=" N LYS A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 4.551A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.552A pdb=" N GLN A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.009A pdb=" N ILE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.562A pdb=" N ALA A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.516A pdb=" N VAL B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 69 removed outlier: 3.735A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.608A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 119 removed outlier: 4.233A pdb=" N VAL C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.637A pdb=" N LYS C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 4.129A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 92 through 122 removed outlier: 3.932A pdb=" N MET D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 4.146A pdb=" N THR D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.143A pdb=" N ALA D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.616A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.529A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 117 removed outlier: 3.551A pdb=" N LEU E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 4.150A pdb=" N ILE E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.538A pdb=" N ALA E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 32 removed outlier: 3.837A pdb=" N VAL F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 27 " --> pdb=" O ASN F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 69 removed outlier: 3.984A pdb=" N LYS F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.983A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.907A pdb=" N ILE G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE G 79 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 121 removed outlier: 4.204A pdb=" N VAL G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE G 98 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 140 through 145 removed outlier: 4.245A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.677A pdb=" N ALA H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 121 removed outlier: 4.012A pdb=" N VAL H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 141 Processing helix chain 'H' and resid 145 through 166 removed outlier: 3.908A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 235 hydrogen bonds 462 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1902 1.33 - 1.45: 4030 1.45 - 1.57: 5478 1.57 - 1.70: 517 1.70 - 1.82: 44 Bond restraints: 11971 Sorted by residual: bond pdb=" C LYS E 145 " pdb=" O LYS E 145 " ideal model delta sigma weight residual 1.236 1.312 -0.075 1.24e-02 6.50e+03 3.70e+01 bond pdb=" N LYS E 145 " pdb=" CA LYS E 145 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 9.92e+00 bond pdb=" N LEU D 117 " pdb=" CA LEU D 117 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.28e-02 6.10e+03 8.99e+00 bond pdb=" N ILE B 14 " pdb=" CA ILE B 14 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.80e+00 bond pdb=" N THR C 136 " pdb=" CA THR C 136 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 ... (remaining 11966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 17055 2.47 - 4.94: 176 4.94 - 7.41: 16 7.41 - 9.87: 2 9.87 - 12.34: 1 Bond angle restraints: 17250 Sorted by residual: angle pdb=" N ASN B 16 " pdb=" CA ASN B 16 " pdb=" C ASN B 16 " ideal model delta sigma weight residual 110.35 98.01 12.34 1.36e+00 5.41e-01 8.24e+01 angle pdb=" N ASP A 126 " pdb=" CA ASP A 126 " pdb=" C ASP A 126 " ideal model delta sigma weight residual 112.90 107.33 5.57 1.31e+00 5.83e-01 1.81e+01 angle pdb=" N SER C 152 " pdb=" CA SER C 152 " pdb=" C SER C 152 " ideal model delta sigma weight residual 107.73 112.51 -4.78 1.34e+00 5.57e-01 1.27e+01 angle pdb=" C ALA E 144 " pdb=" N LYS E 145 " pdb=" CA LYS E 145 " ideal model delta sigma weight residual 120.38 115.37 5.01 1.46e+00 4.69e-01 1.18e+01 angle pdb=" CA GLY C 154 " pdb=" C GLY C 154 " pdb=" O GLY C 154 " ideal model delta sigma weight residual 121.63 117.97 3.66 1.07e+00 8.73e-01 1.17e+01 ... (remaining 17245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 5225 34.21 - 68.43: 1299 68.43 - 102.64: 31 102.64 - 136.85: 1 136.85 - 171.06: 5 Dihedral angle restraints: 6561 sinusoidal: 4335 harmonic: 2226 Sorted by residual: dihedral pdb=" CD ARG G 75 " pdb=" NE ARG G 75 " pdb=" CZ ARG G 75 " pdb=" NH1 ARG G 75 " ideal model delta sinusoidal sigma weight residual 0.00 63.64 -63.64 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CA GLY A 70 " pdb=" C GLY A 70 " pdb=" N ARG A 71 " pdb=" CA ARG A 71 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG A 71 " pdb=" C ARG A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 6558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1734 0.052 - 0.105: 220 0.105 - 0.157: 30 0.157 - 0.209: 6 0.209 - 0.262: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA ASN B 16 " pdb=" N ASN B 16 " pdb=" C ASN B 16 " pdb=" CB ASN B 16 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE D 142 " pdb=" CA ILE D 142 " pdb=" CG1 ILE D 142 " pdb=" CG2 ILE D 142 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA ILE E 138 " pdb=" N ILE E 138 " pdb=" C ILE E 138 " pdb=" CB ILE E 138 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 1988 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 75 " -0.982 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG G 75 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG G 75 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 75 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 75 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 14 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ILE B 14 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 14 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 15 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 143 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C ALA D 143 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA D 143 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 144 " -0.014 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 325 2.66 - 3.22: 9772 3.22 - 3.78: 19471 3.78 - 4.34: 25040 4.34 - 4.90: 36539 Nonbonded interactions: 91147 Sorted by model distance: nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.099 2.496 nonbonded pdb=" NH1 ARG A 119 " pdb=" OD2 ASP A 126 " model vdw 2.184 3.120 nonbonded pdb=" NE2 HIS B 68 " pdb=" OD1 ASP D 130 " model vdw 2.205 3.120 nonbonded pdb=" O TYR G 134 " pdb=" N ASN G 138 " model vdw 2.205 3.120 nonbonded pdb=" O SER F 69 " pdb=" OG SER F 69 " model vdw 2.218 3.040 ... (remaining 91142 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11971 Z= 0.241 Angle : 0.674 12.344 17250 Z= 0.413 Chirality : 0.037 0.262 1991 Planarity : 0.013 0.440 1272 Dihedral : 28.716 171.063 5117 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.63 % Favored : 88.98 % Rotamer: Outliers : 5.54 % Allowed : 33.07 % Favored : 61.39 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -1.00 (0.32), residues: 762 helix: 0.56 (0.25), residues: 485 sheet: None (None), residues: 0 loop : -2.98 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.009 0.001 TYR B 56 PHE 0.012 0.001 PHE C 98 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00416 (11971) covalent geometry : angle 0.67443 (17250) hydrogen bonds : bond 0.10131 ( 532) hydrogen bonds : angle 4.11468 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.284 Fit side-chains REVERT: C 66 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7020 (mpt180) REVERT: C 81 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8328 (tppt) REVERT: C 109 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 104 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6809 (mptt) REVERT: E 52 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8145 (mmmt) REVERT: E 66 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6884 (mpt180) REVERT: E 123 MET cc_start: 0.7594 (mtp) cc_final: 0.7373 (mtp) REVERT: H 97 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (tp30) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.1436 time to fit residues: 30.8513 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN G 83 ASN H 115 ASN H 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111327 restraints weight = 23094.105| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.12 r_work: 0.3699 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11971 Z= 0.154 Angle : 0.574 6.165 17250 Z= 0.332 Chirality : 0.033 0.168 1991 Planarity : 0.004 0.054 1272 Dihedral : 30.587 159.805 3703 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.92 % Favored : 90.42 % Rotamer: Outliers : 6.01 % Allowed : 33.70 % Favored : 60.28 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.47 (0.32), residues: 762 helix: 1.11 (0.25), residues: 481 sheet: None (None), residues: 0 loop : -3.01 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.008 0.001 TYR G 134 PHE 0.014 0.002 PHE F 47 HIS 0.002 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00328 (11971) covalent geometry : angle 0.57398 (17250) hydrogen bonds : bond 0.05070 ( 532) hydrogen bonds : angle 3.15596 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.333 Fit side-chains REVERT: C 81 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8434 (tppt) REVERT: C 109 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 104 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6855 (mptt) REVERT: D 124 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6602 (mt0) REVERT: E 52 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8281 (mmmt) REVERT: E 123 MET cc_start: 0.7602 (mtp) cc_final: 0.7379 (mtp) REVERT: G 140 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7484 (mt-10) REVERT: H 132 ARG cc_start: 0.7999 (tmm-80) cc_final: 0.7651 (ttm170) outliers start: 38 outliers final: 29 residues processed: 163 average time/residue: 0.1261 time to fit residues: 27.0528 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.134395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107000 restraints weight = 23661.568| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.00 r_work: 0.3628 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11971 Z= 0.244 Angle : 0.654 8.520 17250 Z= 0.374 Chirality : 0.038 0.201 1991 Planarity : 0.005 0.052 1272 Dihedral : 30.897 153.162 3665 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.24 % Favored : 89.24 % Rotamer: Outliers : 10.92 % Allowed : 30.38 % Favored : 58.70 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.70 (0.32), residues: 762 helix: 0.89 (0.25), residues: 483 sheet: None (None), residues: 0 loop : -3.03 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.011 0.002 TYR G 134 PHE 0.017 0.002 PHE C 98 HIS 0.004 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00551 (11971) covalent geometry : angle 0.65397 (17250) hydrogen bonds : bond 0.06378 ( 532) hydrogen bonds : angle 3.40789 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 0.301 Fit side-chains REVERT: B 49 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8382 (mtmm) REVERT: B 60 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: C 81 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8337 (tppt) REVERT: C 109 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7592 (tm-30) REVERT: D 104 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6925 (mptt) REVERT: D 124 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: E 52 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8239 (mmmt) REVERT: F 71 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7096 (mtm-85) REVERT: G 140 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7748 (mt-10) REVERT: G 153 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.6016 (p-80) REVERT: H 132 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7697 (ttm170) outliers start: 69 outliers final: 51 residues processed: 179 average time/residue: 0.1237 time to fit residues: 29.3516 Evaluate side-chains 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.137835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109953 restraints weight = 23250.771| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.16 r_work: 0.3678 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11971 Z= 0.155 Angle : 0.584 7.134 17250 Z= 0.337 Chirality : 0.034 0.136 1991 Planarity : 0.004 0.055 1272 Dihedral : 30.675 153.883 3665 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.92 % Favored : 90.55 % Rotamer: Outliers : 8.23 % Allowed : 32.12 % Favored : 59.65 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.24 (0.32), residues: 762 helix: 1.33 (0.25), residues: 475 sheet: None (None), residues: 0 loop : -2.89 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 144 TYR 0.009 0.001 TYR F 56 PHE 0.013 0.002 PHE F 47 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00331 (11971) covalent geometry : angle 0.58401 (17250) hydrogen bonds : bond 0.04959 ( 532) hydrogen bonds : angle 3.06485 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.334 Fit side-chains REVERT: B 49 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: C 81 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8382 (tppt) REVERT: C 109 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: C 146 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4983 (pp) REVERT: D 104 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6771 (mptt) REVERT: D 158 LYS cc_start: 0.8183 (tppt) cc_final: 0.7942 (tptt) REVERT: E 52 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8199 (mmmt) REVERT: G 140 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7548 (mt-10) REVERT: H 132 ARG cc_start: 0.8007 (tmm-80) cc_final: 0.7657 (ttm170) outliers start: 52 outliers final: 39 residues processed: 168 average time/residue: 0.1300 time to fit residues: 28.7954 Evaluate side-chains 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.0170 chunk 64 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN G 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.111865 restraints weight = 23237.772| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.16 r_work: 0.3704 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11971 Z= 0.146 Angle : 0.570 6.846 17250 Z= 0.330 Chirality : 0.033 0.137 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.565 153.538 3661 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.92 % Favored : 90.55 % Rotamer: Outliers : 7.59 % Allowed : 32.75 % Favored : 59.65 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.08 (0.33), residues: 762 helix: 1.47 (0.25), residues: 475 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.008 0.001 TYR F 56 PHE 0.012 0.001 PHE F 47 HIS 0.003 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00308 (11971) covalent geometry : angle 0.57031 (17250) hydrogen bonds : bond 0.04681 ( 532) hydrogen bonds : angle 2.98953 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.298 Fit side-chains REVERT: B 49 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8339 (mtmm) REVERT: C 81 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8434 (tppt) REVERT: C 109 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: C 146 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4685 (pp) REVERT: D 124 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6666 (mt0) REVERT: D 158 LYS cc_start: 0.8168 (tppt) cc_final: 0.7927 (tptt) REVERT: E 52 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8213 (mmmt) REVERT: E 123 MET cc_start: 0.7411 (mtp) cc_final: 0.7183 (mtp) REVERT: G 140 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7444 (mt-10) outliers start: 48 outliers final: 37 residues processed: 161 average time/residue: 0.1364 time to fit residues: 28.8112 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106861 restraints weight = 23566.673| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.01 r_work: 0.3628 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11971 Z= 0.249 Angle : 0.667 6.649 17250 Z= 0.380 Chirality : 0.038 0.142 1991 Planarity : 0.005 0.053 1272 Dihedral : 30.882 150.963 3653 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.24 % Favored : 89.37 % Rotamer: Outliers : 10.60 % Allowed : 30.38 % Favored : 59.02 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.32), residues: 762 helix: 0.84 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.02 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.012 0.002 TYR B 56 PHE 0.018 0.003 PHE H 91 HIS 0.004 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00564 (11971) covalent geometry : angle 0.66702 (17250) hydrogen bonds : bond 0.06363 ( 532) hydrogen bonds : angle 3.34806 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 118 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 49 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (mtmm) REVERT: B 60 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7845 (m-40) REVERT: C 81 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8284 (tppt) REVERT: C 105 ASP cc_start: 0.8214 (t0) cc_final: 0.7850 (m-30) REVERT: C 109 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: D 104 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6953 (mptt) REVERT: D 124 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6746 (mt0) REVERT: E 52 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8247 (mmmt) REVERT: G 140 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7669 (mt-10) REVERT: G 153 HIS cc_start: 0.6325 (OUTLIER) cc_final: 0.6022 (p-80) REVERT: H 96 MET cc_start: 0.8437 (mmm) cc_final: 0.8183 (tpp) REVERT: H 124 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6382 (pm20) outliers start: 67 outliers final: 49 residues processed: 169 average time/residue: 0.1216 time to fit residues: 27.5346 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.109724 restraints weight = 23380.775| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.16 r_work: 0.3671 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11971 Z= 0.161 Angle : 0.597 7.002 17250 Z= 0.344 Chirality : 0.034 0.146 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.676 151.074 3653 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.10 % Favored : 89.37 % Rotamer: Outliers : 8.54 % Allowed : 32.91 % Favored : 58.54 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.36 (0.32), residues: 762 helix: 1.21 (0.25), residues: 479 sheet: None (None), residues: 0 loop : -2.96 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 132 TYR 0.010 0.001 TYR F 56 PHE 0.013 0.001 PHE H 91 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00350 (11971) covalent geometry : angle 0.59700 (17250) hydrogen bonds : bond 0.05032 ( 532) hydrogen bonds : angle 3.09543 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 49 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: C 81 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8407 (tppt) REVERT: C 105 ASP cc_start: 0.8116 (t0) cc_final: 0.7879 (m-30) REVERT: C 109 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: D 124 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6678 (mt0) REVERT: E 52 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8241 (mmmt) REVERT: G 59 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6930 (t0) REVERT: G 140 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7555 (mt-10) REVERT: H 96 MET cc_start: 0.8300 (mmm) cc_final: 0.8068 (tpp) REVERT: H 132 ARG cc_start: 0.8034 (tmm-80) cc_final: 0.7831 (ttm-80) outliers start: 54 outliers final: 45 residues processed: 161 average time/residue: 0.1279 time to fit residues: 27.3879 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.136451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108811 restraints weight = 23292.021| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.13 r_work: 0.3655 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11971 Z= 0.181 Angle : 0.619 8.151 17250 Z= 0.353 Chirality : 0.035 0.156 1991 Planarity : 0.004 0.055 1272 Dihedral : 30.703 149.474 3653 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.24 % Favored : 89.24 % Rotamer: Outliers : 9.34 % Allowed : 32.44 % Favored : 58.23 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.41 (0.32), residues: 762 helix: 1.20 (0.25), residues: 479 sheet: None (None), residues: 0 loop : -3.03 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 123 TYR 0.009 0.001 TYR B 56 PHE 0.015 0.002 PHE H 91 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00400 (11971) covalent geometry : angle 0.61911 (17250) hydrogen bonds : bond 0.05319 ( 532) hydrogen bonds : angle 3.13631 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 49 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8407 (mtmm) REVERT: C 81 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8297 (tppt) REVERT: C 105 ASP cc_start: 0.8152 (t0) cc_final: 0.7926 (m-30) REVERT: C 109 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: D 104 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6890 (mptt) REVERT: D 124 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6681 (mt0) REVERT: G 59 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.7005 (t0) REVERT: G 140 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7572 (mt-10) REVERT: H 96 MET cc_start: 0.8414 (mmm) cc_final: 0.8203 (tpp) REVERT: H 132 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7820 (ttm-80) outliers start: 59 outliers final: 49 residues processed: 162 average time/residue: 0.1248 time to fit residues: 27.0802 Evaluate side-chains 174 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.0070 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107436 restraints weight = 23259.955| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.97 r_work: 0.3637 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11971 Z= 0.220 Angle : 0.662 8.180 17250 Z= 0.375 Chirality : 0.037 0.165 1991 Planarity : 0.004 0.054 1272 Dihedral : 30.854 146.932 3649 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.37 % Favored : 89.24 % Rotamer: Outliers : 9.65 % Allowed : 32.28 % Favored : 58.07 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.75 (0.32), residues: 762 helix: 0.83 (0.24), residues: 491 sheet: None (None), residues: 0 loop : -3.12 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 71 TYR 0.012 0.001 TYR A 102 PHE 0.018 0.002 PHE H 91 HIS 0.003 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00495 (11971) covalent geometry : angle 0.66150 (17250) hydrogen bonds : bond 0.05982 ( 532) hydrogen bonds : angle 3.30144 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: C 81 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8285 (tppt) REVERT: C 105 ASP cc_start: 0.8232 (t0) cc_final: 0.7982 (m-30) REVERT: C 109 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: D 104 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6876 (mptt) REVERT: D 124 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: E 123 MET cc_start: 0.7593 (mtp) cc_final: 0.7329 (mtp) REVERT: G 140 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7648 (mt-10) REVERT: H 124 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6541 (pm20) outliers start: 61 outliers final: 51 residues processed: 166 average time/residue: 0.1127 time to fit residues: 25.2744 Evaluate side-chains 173 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107870 restraints weight = 23434.636| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.00 r_work: 0.3643 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11971 Z= 0.214 Angle : 0.672 8.975 17250 Z= 0.378 Chirality : 0.036 0.145 1991 Planarity : 0.005 0.054 1272 Dihedral : 30.846 146.435 3649 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.50 % Favored : 88.85 % Rotamer: Outliers : 9.18 % Allowed : 32.75 % Favored : 58.07 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.31), residues: 762 helix: 0.72 (0.24), residues: 492 sheet: None (None), residues: 0 loop : -3.17 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 132 TYR 0.013 0.002 TYR A 102 PHE 0.015 0.002 PHE C 98 HIS 0.003 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00481 (11971) covalent geometry : angle 0.67189 (17250) hydrogen bonds : bond 0.05775 ( 532) hydrogen bonds : angle 3.31990 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 49 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: B 60 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7752 (m-40) REVERT: B 80 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7061 (ttp-170) REVERT: C 81 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8313 (tppt) REVERT: C 105 ASP cc_start: 0.8227 (t0) cc_final: 0.8001 (m-30) REVERT: C 109 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: D 104 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6865 (mptt) REVERT: D 124 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6810 (mt0) REVERT: E 123 MET cc_start: 0.7588 (mtp) cc_final: 0.7331 (mtp) REVERT: G 140 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7650 (mt-10) REVERT: H 124 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6564 (pm20) outliers start: 58 outliers final: 50 residues processed: 165 average time/residue: 0.1186 time to fit residues: 25.9951 Evaluate side-chains 178 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 40 optimal weight: 0.0470 chunk 18 optimal weight: 0.0030 overall best weight: 0.2406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.135262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108096 restraints weight = 23597.122| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.02 r_work: 0.3647 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11971 Z= 0.200 Angle : 0.886 59.199 17250 Z= 0.518 Chirality : 0.042 1.024 1991 Planarity : 0.005 0.053 1272 Dihedral : 30.854 146.447 3647 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.50 % Favored : 88.85 % Rotamer: Outliers : 9.34 % Allowed : 32.12 % Favored : 58.54 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.31), residues: 762 helix: 0.78 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -3.13 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 144 TYR 0.013 0.001 TYR A 102 PHE 0.016 0.002 PHE H 91 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00436 (11971) covalent geometry : angle 0.88552 (17250) hydrogen bonds : bond 0.05668 ( 532) hydrogen bonds : angle 3.31277 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.07 seconds wall clock time: 43 minutes 7.03 seconds (2587.03 seconds total)