Starting phenix.real_space_refine on Wed Aug 5 17:51:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua7_42053/08_2026/8ua7_42053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua7_42053/08_2026/8ua7_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_2026/8ua7_42053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2026/8ua7_42053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2026/8ua7_42053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua7_42053/08_2026/8ua7_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-2.2rc3-6140/lib/python3.11/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: 1.87, per 1000 atoms: 0.17 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: 0.87 Conformation dependent library (CDL) restraints added in 198.5 milliseconds 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: 1.33 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: 1.36 Time building geometry restraints manager: 1.09 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=" C3' DG J -60 " pdb=" C2' DG J -60 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT I 69 " pdb=" C2' DT I 69 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 11966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 16960 2.47 - 4.94: 271 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=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT J -6 " pdb=" C4 DT J -6 " pdb=" O4 DT J -6 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+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: 1543 0.052 - 0.105: 388 0.105 - 0.157: 52 0.157 - 0.209: 7 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=" C3' DT J -68 " pdb=" C4' DT J -68 " pdb=" O3' DT J -68 " pdb=" C2' DT J -68 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.18 2.00e-01 2.50e+01 7.68e-01 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 ... (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: 2.350 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.006 0.075 11971 Z= 0.520 Angle : 0.820 12.344 17250 Z= 0.681 Chirality : 0.047 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 are 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/Z covalent geometry : bond 0.00587 / 0.52 (11971) covalent geometry : angle 0.81953 / 0.68 (17250) hydrogen bonds : bond 0.10131 / 6.73 ( 532) hydrogen bonds : angle 4.11468 / 2.92 ( 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 : 0.240 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: 0.8144 (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) REVERT: H 124 GLN cc_start: 0.6198 (OUTLIER) cc_final: 0.5796 (pm20) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.1311 time to fit residues: 28.2964 Evaluate side-chains 162 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 124 GLN 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: 9.9990 chunk 53 optimal weight: 0.9980 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: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN G 83 ASN H 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110622 restraints weight = 22982.843| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.13 r_work: 0.3688 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11971 Z= 0.153 Angle : 0.642 6.467 17250 Z= 0.373 Chirality : 0.044 0.348 1991 Planarity : 0.005 0.055 1272 Dihedral : 30.845 164.212 3706 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.66 % Favored : 90.68 % Rotamer: Outliers : 6.96 % Allowed : 33.86 % Favored : 59.18 % 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 are not related in a simple way. whole: -0.76 (0.32), residues: 762 helix: 0.79 (0.25), residues: 494 sheet: None (None), residues: 0 loop : -3.12 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 144 TYR 0.010 0.001 TYR G 134 PHE 0.012 0.002 PHE C 98 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (11971) covalent geometry : angle 0.64231 / 0.37 (17250) hydrogen bonds : bond 0.05967 / 4.09 ( 532) hydrogen bonds : angle 3.31844 / 2.34 ( 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 177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.215 Fit side-chains REVERT: C 81 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8343 (tppt) REVERT: C 109 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 104 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6819 (mptt) REVERT: D 124 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6504 (mt0) REVERT: E 52 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8201 (mmmt) REVERT: E 123 MET cc_start: 0.7657 (mtp) cc_final: 0.7407 (mtp) REVERT: G 140 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7528 (mt-10) REVERT: H 132 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7636 (ttm170) outliers start: 44 outliers final: 35 residues processed: 166 average time/residue: 0.1269 time to fit residues: 27.9709 Evaluate side-chains 165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 20 GLU 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 136 THR 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 113 VAL 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 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN 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: 2.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.133919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106314 restraints weight = 23568.860| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.99 r_work: 0.3616 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11971 Z= 0.246 Angle : 0.742 8.260 17250 Z= 0.420 Chirality : 0.048 0.373 1991 Planarity : 0.005 0.050 1272 Dihedral : 31.091 156.782 3669 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.55 % Favored : 87.93 % Rotamer: Outliers : 12.18 % Allowed : 28.64 % Favored : 59.18 % 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 are not related in a simple way. whole: -1.09 (0.31), residues: 762 helix: 0.55 (0.25), residues: 487 sheet: None (None), residues: 0 loop : -3.18 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 144 TYR 0.017 0.002 TYR G 134 PHE 0.018 0.003 PHE B 47 HIS 0.005 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.25 (11971) covalent geometry : angle 0.74232 / 0.42 (17250) hydrogen bonds : bond 0.07406 / 4.91 ( 532) hydrogen bonds : angle 3.63400 / 2.57 ( 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 207 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 130 time to evaluate : 0.221 Fit side-chains REVERT: B 49 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8338 (mtmm) REVERT: B 60 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: C 81 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8344 (tppt) REVERT: C 109 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 104 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6960 (mptt) REVERT: D 124 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6653 (mt0) REVERT: D 155 MET cc_start: 0.7359 (tpp) cc_final: 0.7088 (tpt) REVERT: E 52 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8255 (mmmt) REVERT: E 123 MET cc_start: 0.7826 (mtp) cc_final: 0.7554 (mtp) REVERT: F 71 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7127 (mtm-85) REVERT: G 140 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7718 (mt-10) REVERT: G 153 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5986 (p-80) REVERT: H 132 ARG cc_start: 0.8129 (tmm-80) cc_final: 0.7654 (ttm170) outliers start: 77 outliers final: 56 residues processed: 190 average time/residue: 0.1209 time to fit residues: 30.7504 Evaluate side-chains 187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 60 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE 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 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 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL 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 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER 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 39 LEU 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 78 LYS 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 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 124 GLN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 115 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110096 restraints weight = 23320.632| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.01 r_work: 0.3687 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11971 Z= 0.145 Angle : 0.641 7.110 17250 Z= 0.369 Chirality : 0.043 0.363 1991 Planarity : 0.004 0.055 1272 Dihedral : 30.972 157.471 3666 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.06 % Favored : 90.42 % Rotamer: Outliers : 8.70 % Allowed : 32.91 % Favored : 58.39 % 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 are not related in a simple way. whole: -0.52 (0.32), residues: 762 helix: 1.07 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.01 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 132 TYR 0.010 0.001 TYR A 102 PHE 0.019 0.002 PHE H 91 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (11971) covalent geometry : angle 0.64108 / 0.37 (17250) hydrogen bonds : bond 0.05655 / 3.90 ( 532) hydrogen bonds : angle 3.22775 / 2.27 ( 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 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.254 Fit side-chains REVERT: B 49 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8275 (mtmm) REVERT: C 81 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8371 (tppt) REVERT: C 109 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 104 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6834 (mptt) REVERT: D 124 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6621 (mt0) REVERT: E 123 MET cc_start: 0.7538 (mtp) cc_final: 0.7195 (mtp) REVERT: G 140 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7578 (mt-10) outliers start: 55 outliers final: 42 residues processed: 166 average time/residue: 0.1167 time to fit residues: 26.2247 Evaluate side-chains 170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL 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 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 132 THR 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 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 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 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4173 r_free = 0.4173 target = 0.136192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108785 restraints weight = 23359.735| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.00 r_work: 0.3658 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11971 Z= 0.170 Angle : 0.658 6.900 17250 Z= 0.376 Chirality : 0.044 0.368 1991 Planarity : 0.004 0.056 1272 Dihedral : 31.016 156.375 3666 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 9.65 % Allowed : 31.96 % Favored : 58.39 % 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 are not related in a simple way. whole: -0.53 (0.32), residues: 762 helix: 1.03 (0.25), residues: 483 sheet: None (None), residues: 0 loop : -3.00 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 144 TYR 0.011 0.001 TYR G 134 PHE 0.022 0.002 PHE H 91 HIS 0.003 0.000 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (11971) covalent geometry : angle 0.65814 / 0.38 (17250) hydrogen bonds : bond 0.06043 / 4.10 ( 532) hydrogen bonds : angle 3.26993 / 2.31 ( 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 190 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.299 Fit side-chains REVERT: B 49 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8375 (mtmm) REVERT: C 81 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8367 (tppt) REVERT: C 109 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 104 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6861 (mptt) REVERT: D 124 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: D 155 MET cc_start: 0.7344 (tpp) cc_final: 0.7020 (tpt) REVERT: E 52 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8204 (mmmt) REVERT: E 123 MET cc_start: 0.7618 (mtp) cc_final: 0.7232 (mtp) REVERT: G 140 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7615 (mt-10) REVERT: H 132 ARG cc_start: 0.8013 (tmm-80) cc_final: 0.7592 (ttm-80) outliers start: 61 outliers final: 49 residues processed: 172 average time/residue: 0.1196 time to fit residues: 28.0386 Evaluate side-chains 176 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 50 VAL 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 94 THR 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 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 149 VAL 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 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 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 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 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 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE 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: 0.6980 chunk 74 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 115 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109140 restraints weight = 23436.363| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.99 r_work: 0.3666 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11971 Z= 0.160 Angle : 0.650 7.109 17250 Z= 0.371 Chirality : 0.044 0.372 1991 Planarity : 0.004 0.055 1272 Dihedral : 31.030 156.026 3666 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.84 % Favored : 89.63 % Rotamer: Outliers : 10.44 % Allowed : 31.49 % 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 are not related in a simple way. whole: -0.52 (0.32), residues: 762 helix: 1.03 (0.25), residues: 484 sheet: None (None), residues: 0 loop : -2.98 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 144 TYR 0.009 0.001 TYR B 56 PHE 0.017 0.002 PHE H 91 HIS 0.002 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (11971) covalent geometry : angle 0.64951 / 0.37 (17250) hydrogen bonds : bond 0.05828 / 3.98 ( 532) hydrogen bonds : angle 3.23376 / 2.28 ( 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 194 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 0.226 Fit side-chains REVERT: B 49 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8370 (mtmm) REVERT: B 60 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: C 81 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8372 (tppt) REVERT: C 109 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: D 104 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6877 (mptt) REVERT: D 124 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6679 (mt0) REVERT: E 52 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8217 (mmmt) REVERT: E 123 MET cc_start: 0.7559 (mtp) cc_final: 0.7183 (mtp) REVERT: G 140 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7593 (mt-10) outliers start: 66 outliers final: 53 residues processed: 175 average time/residue: 0.1177 time to fit residues: 27.9519 Evaluate side-chains 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 50 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 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 149 VAL 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 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 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 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 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 110 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4182 r_free = 0.4182 target = 0.136786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109006 restraints weight = 23305.668| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.13 r_work: 0.3656 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11971 Z= 0.156 Angle : 0.647 7.925 17250 Z= 0.370 Chirality : 0.044 0.368 1991 Planarity : 0.004 0.056 1272 Dihedral : 31.016 155.833 3666 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.24 % Favored : 89.24 % Rotamer: Outliers : 9.81 % Allowed : 32.12 % 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 are not related in a simple way. whole: -0.51 (0.32), residues: 762 helix: 1.05 (0.25), residues: 484 sheet: None (None), residues: 0 loop : -3.00 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 144 TYR 0.009 0.001 TYR F 56 PHE 0.016 0.002 PHE H 91 HIS 0.002 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (11971) covalent geometry : angle 0.64700 / 0.37 (17250) hydrogen bonds : bond 0.05709 / 3.90 ( 532) hydrogen bonds : angle 3.21974 / 2.27 ( 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 190 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 0.260 Fit side-chains REVERT: B 49 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8415 (mtmm) REVERT: B 60 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7787 (m-40) REVERT: C 81 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8343 (tppt) REVERT: C 109 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: D 104 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6873 (mptt) REVERT: D 124 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6678 (mt0) REVERT: D 155 MET cc_start: 0.7240 (tpp) cc_final: 0.6954 (tpt) REVERT: E 52 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8223 (mmmt) REVERT: E 123 MET cc_start: 0.7530 (mtp) cc_final: 0.7143 (mtp) REVERT: G 140 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 132 ARG cc_start: 0.7998 (tmm-80) cc_final: 0.7786 (ttm-80) outliers start: 62 outliers final: 52 residues processed: 170 average time/residue: 0.1147 time to fit residues: 26.4887 Evaluate side-chains 183 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 79 LEU Chi-restraints excluded: chain D residue 104 LYS 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 149 VAL 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 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 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 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 110 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 ASN G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.138562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110870 restraints weight = 22874.772| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.13 r_work: 0.3692 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11971 Z= 0.138 Angle : 0.630 7.965 17250 Z= 0.360 Chirality : 0.042 0.372 1991 Planarity : 0.004 0.055 1272 Dihedral : 30.951 156.073 3664 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.45 % Favored : 90.03 % Rotamer: Outliers : 9.18 % Allowed : 33.07 % Favored : 57.75 % 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 are not related in a simple way. whole: -0.26 (0.32), residues: 762 helix: 1.33 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.009 0.001 TYR F 56 PHE 0.011 0.001 PHE C 98 HIS 0.003 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (11971) covalent geometry : angle 0.63018 / 0.36 (17250) hydrogen bonds : bond 0.05243 / 3.62 ( 532) hydrogen bonds : angle 3.10033 / 2.17 ( 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 189 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.237 Fit side-chains REVERT: B 49 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8407 (mtmm) REVERT: B 60 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7840 (m-40) REVERT: C 81 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8237 (tppt) REVERT: C 109 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: D 104 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6776 (mptt) REVERT: D 124 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6615 (mt0) REVERT: D 155 MET cc_start: 0.7166 (tpp) cc_final: 0.6887 (tpt) REVERT: E 52 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8187 (mmmt) REVERT: E 123 MET cc_start: 0.7507 (mtp) cc_final: 0.7058 (mtp) REVERT: G 140 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7570 (mt-10) outliers start: 58 outliers final: 48 residues processed: 171 average time/residue: 0.1063 time to fit residues: 24.7688 Evaluate side-chains 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU 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 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 109 GLU Chi-restraints excluded: chain C residue 124 ILE 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 149 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 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 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 57 GLU Chi-restraints excluded: chain F residue 60 ASN 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 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 110 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 142 HIS G 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105791 restraints weight = 23035.471| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.13 r_work: 0.3607 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11971 Z= 0.248 Angle : 0.761 8.850 17250 Z= 0.422 Chirality : 0.048 0.379 1991 Planarity : 0.005 0.054 1272 Dihedral : 31.155 154.434 3662 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.02 % Favored : 88.32 % 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 are not related in a simple way. whole: -0.92 (0.32), residues: 762 helix: 0.67 (0.25), residues: 483 sheet: None (None), residues: 0 loop : -3.02 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.016 0.002 TYR G 134 PHE 0.031 0.003 PHE H 91 HIS 0.005 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 (11971) covalent geometry : angle 0.76072 / 0.42 (17250) hydrogen bonds : bond 0.07077 / 4.71 ( 532) hydrogen bonds : angle 3.54080 / 2.51 ( 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 183 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.296 Fit side-chains REVERT: B 49 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8467 (mtmm) REVERT: B 60 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7921 (m-40) REVERT: C 81 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8246 (tppt) REVERT: C 109 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: D 104 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6922 (mptt) REVERT: D 123 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7528 (ttp-170) REVERT: D 124 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: E 123 MET cc_start: 0.7723 (mtp) cc_final: 0.7301 (mtp) REVERT: G 140 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7768 (mt-10) outliers start: 59 outliers final: 46 residues processed: 170 average time/residue: 0.1266 time to fit residues: 29.0387 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU 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 123 ARG Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 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 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 88 ILE 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 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 142 HIS G 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.136732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.109175 restraints weight = 23313.928| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.13 r_work: 0.3652 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11971 Z= 0.158 Angle : 0.682 8.444 17250 Z= 0.383 Chirality : 0.044 0.374 1991 Planarity : 0.004 0.055 1272 Dihedral : 31.095 154.765 3662 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.58 % Favored : 89.76 % Rotamer: Outliers : 8.54 % Allowed : 34.02 % Favored : 57.44 % 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 are not related in a simple way. whole: -0.68 (0.32), residues: 762 helix: 0.88 (0.25), residues: 485 sheet: None (None), residues: 0 loop : -3.00 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 132 TYR 0.010 0.001 TYR F 56 PHE 0.020 0.002 PHE H 91 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (11971) covalent geometry : angle 0.68187 / 0.38 (17250) hydrogen bonds : bond 0.05831 / 3.98 ( 532) hydrogen bonds : angle 3.25621 / 2.29 ( 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 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.209 Fit side-chains REVERT: B 49 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8417 (mtmm) REVERT: B 60 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7777 (m-40) REVERT: C 81 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8321 (tppt) REVERT: C 109 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: D 104 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6847 (mptt) REVERT: D 124 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6736 (mt0) REVERT: E 123 MET cc_start: 0.7433 (mtp) cc_final: 0.7038 (mtp) REVERT: G 140 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7614 (mt-10) outliers start: 54 outliers final: 47 residues processed: 168 average time/residue: 0.1124 time to fit residues: 25.4603 Evaluate side-chains 175 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 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 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 146 LEU 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 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 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 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 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 88 ILE Chi-restraints excluded: chain G residue 110 ILE 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 102 ILE Chi-restraints excluded: chain H residue 110 MET 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: 9.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4201 r_free = 0.4201 target = 0.138114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110470 restraints weight = 23252.219| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.17 r_work: 0.3686 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11971 Z= 0.140 Angle : 0.657 9.478 17250 Z= 0.371 Chirality : 0.043 0.373 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.980 155.168 3660 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.97 % Favored : 89.37 % Rotamer: Outliers : 7.91 % Allowed : 35.28 % Favored : 56.80 % 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 are not related in a simple way. whole: -0.42 (0.32), residues: 762 helix: 1.20 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -2.97 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.010 0.001 TYR F 56 PHE 0.012 0.001 PHE C 98 HIS 0.003 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (11971) covalent geometry : angle 0.65731 / 0.37 (17250) hydrogen bonds : bond 0.05249 / 3.62 ( 532) hydrogen bonds : angle 3.12311 / 2.19 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.93 seconds wall clock time: 40 minutes 45.69 seconds (2445.69 seconds total)