Starting phenix.real_space_refine on Fri Jul 3 00:03:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua7_42053/07_2026/8ua7_42053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua7_42053/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua7_42053/07_2026/8ua7_42053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua7_42053/07_2026/8ua7_42053.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua7_42053/07_2026/8ua7_42053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua7_42053/07_2026/8ua7_42053.cif" } 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-dev-6108/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: 2.34, per 1000 atoms: 0.21 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: 0.88 Conformation dependent library (CDL) restraints added in 258.9 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: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.522A pdb=" N LYS A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 4.551A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.552A pdb=" N GLN A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.009A pdb=" N ILE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.562A pdb=" N ALA A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.516A pdb=" N VAL B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 69 removed outlier: 3.735A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.608A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 119 removed outlier: 4.233A pdb=" N VAL C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.637A pdb=" N LYS C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 4.129A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 92 through 122 removed outlier: 3.932A pdb=" N MET D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 4.146A pdb=" N THR D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.143A pdb=" N ALA D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.616A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.529A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 117 removed outlier: 3.551A pdb=" N LEU E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 4.150A pdb=" N ILE E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.538A pdb=" N ALA E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 32 removed outlier: 3.837A pdb=" N VAL F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 27 " --> pdb=" O ASN F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 69 removed outlier: 3.984A pdb=" N LYS F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.983A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.907A pdb=" N ILE G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE G 79 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 121 removed outlier: 4.204A pdb=" N VAL G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE G 98 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 140 through 145 removed outlier: 4.245A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.677A pdb=" N ALA H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 121 removed outlier: 4.012A pdb=" N VAL H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN H 121 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 141 Processing helix chain 'H' and resid 145 through 166 removed outlier: 3.908A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 235 hydrogen bonds 462 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.27 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: 16963 2.47 - 4.94: 268 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- 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 : 0.814 12.344 17250 Z= 0.676 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 0.81433 / 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 : 0.301 Fit side-chains REVERT: C 66 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7020 (mpt180) REVERT: C 81 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8328 (tppt) REVERT: C 109 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 104 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6809 (mptt) REVERT: E 52 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8145 (mmmt) REVERT: E 66 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6884 (mpt180) REVERT: E 123 MET cc_start: 0.7594 (mtp) cc_final: 0.7373 (mtp) REVERT: H 97 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (tp30) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.1520 time to fit residues: 33.0365 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN G 83 ASN H 115 ASN H 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111152 restraints weight = 23053.197| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.14 r_work: 0.3696 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0781 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= 0.148 Angle : 0.622 6.311 17250 Z= 0.367 Chirality : 0.042 0.318 1991 Planarity : 0.004 0.055 1272 Dihedral : 30.886 164.213 3703 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.79 % Favored : 90.55 % Rotamer: Outliers : 6.80 % Allowed : 33.86 % Favored : 59.34 % 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: -0.72 (0.32), residues: 762 helix: 0.81 (0.25), residues: 494 sheet: None (None), residues: 0 loop : -3.07 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 144 TYR 0.008 0.001 TYR G 134 PHE 0.011 0.002 PHE C 98 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.15 (11971) covalent geometry : angle 0.62196 / 0.37 (17250) hydrogen bonds : bond 0.05866 / 4.03 ( 532) hydrogen bonds : angle 3.30397 / 2.33 ( 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 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.227 Fit side-chains REVERT: C 81 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8316 (tppt) REVERT: C 109 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 104 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6819 (mptt) REVERT: D 124 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6613 (mt0) REVERT: E 52 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8206 (mmmt) REVERT: E 123 MET cc_start: 0.7635 (mtp) cc_final: 0.7375 (mtp) REVERT: G 140 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7488 (mt-10) REVERT: H 132 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7629 (ttm170) outliers start: 43 outliers final: 33 residues processed: 169 average time/residue: 0.1483 time to fit residues: 33.0502 Evaluate side-chains 165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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 130 ASP 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: 0.0870 chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.137652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109820 restraints weight = 23300.448| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.11 r_work: 0.3680 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11971 Z= 0.160 Angle : 0.629 7.712 17250 Z= 0.367 Chirality : 0.043 0.335 1991 Planarity : 0.004 0.054 1272 Dihedral : 30.952 163.516 3666 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.45 % Favored : 89.90 % Rotamer: Outliers : 9.02 % Allowed : 30.70 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.32), residues: 762 helix: 1.20 (0.25), residues: 470 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.011 0.001 TYR G 134 PHE 0.019 0.002 PHE H 91 HIS 0.002 0.000 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (11971) covalent geometry : angle 0.62915 / 0.37 (17250) hydrogen bonds : bond 0.05843 / 3.97 ( 532) hydrogen bonds : angle 3.25200 / 2.29 ( 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 183 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.231 Fit side-chains REVERT: C 81 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8439 (tppt) REVERT: C 109 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7606 (tm-30) REVERT: D 104 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6902 (mptt) REVERT: D 124 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6652 (mt0) REVERT: D 155 MET cc_start: 0.7322 (tpp) cc_final: 0.6963 (tpt) REVERT: E 52 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8238 (mmmt) REVERT: E 123 MET cc_start: 0.7631 (mtp) cc_final: 0.7301 (mtp) REVERT: F 71 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6954 (mtp180) REVERT: G 140 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7601 (mt-10) REVERT: H 132 ARG cc_start: 0.7931 (tmm-80) cc_final: 0.7583 (ttm170) outliers start: 57 outliers final: 43 residues processed: 172 average time/residue: 0.1402 time to fit residues: 32.1561 Evaluate side-chains 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR 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 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 36 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 71 ARG 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 142 ILE Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 115 ASN H 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.110249 restraints weight = 23379.341| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.99 r_work: 0.3688 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11971 Z= 0.154 Angle : 0.618 6.618 17250 Z= 0.361 Chirality : 0.042 0.333 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.964 157.736 3665 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.45 % Favored : 90.03 % Rotamer: Outliers : 10.76 % Allowed : 29.59 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.32), residues: 762 helix: 1.34 (0.25), residues: 472 sheet: None (None), residues: 0 loop : -2.95 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.009 0.001 TYR G 134 PHE 0.013 0.002 PHE C 98 HIS 0.002 0.000 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (11971) covalent geometry : angle 0.61839 / 0.36 (17250) hydrogen bonds : bond 0.05660 / 3.87 ( 532) hydrogen bonds : angle 3.20012 / 2.26 ( 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 198 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 0.280 Fit side-chains REVERT: B 60 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7800 (m-40) REVERT: C 81 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8435 (tppt) REVERT: C 109 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 146 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.5159 (pp) REVERT: D 104 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6871 (mptt) REVERT: D 124 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: E 123 MET cc_start: 0.7609 (mtp) cc_final: 0.7284 (mtp) REVERT: G 140 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7544 (mt-10) REVERT: H 97 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: H 132 ARG cc_start: 0.7906 (tmm-80) cc_final: 0.7570 (ttm170) outliers start: 68 outliers final: 50 residues processed: 182 average time/residue: 0.1294 time to fit residues: 31.8798 Evaluate side-chains 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 20 GLU 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 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 92 SER 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 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 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110923 restraints weight = 23333.721| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.17 r_work: 0.3688 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11971 Z= 0.138 Angle : 0.605 7.089 17250 Z= 0.353 Chirality : 0.041 0.341 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.947 158.833 3665 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.32 % Favored : 90.16 % Rotamer: Outliers : 9.34 % Allowed : 31.01 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.32), residues: 762 helix: 1.41 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -2.89 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 32 TYR 0.007 0.001 TYR B 56 PHE 0.014 0.002 PHE H 91 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (11971) covalent geometry : angle 0.60485 / 0.35 (17250) hydrogen bonds : bond 0.05353 / 3.69 ( 532) hydrogen bonds : angle 3.09265 / 2.17 ( 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 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 0.303 Fit side-chains REVERT: C 81 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8444 (tppt) REVERT: C 109 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 146 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.5037 (pp) REVERT: D 124 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: D 155 MET cc_start: 0.7248 (tpp) cc_final: 0.6930 (tpt) REVERT: E 123 MET cc_start: 0.7524 (mtp) cc_final: 0.7120 (mtp) REVERT: G 140 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7574 (mt-10) REVERT: H 97 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7398 (tp30) outliers start: 59 outliers final: 49 residues processed: 169 average time/residue: 0.1213 time to fit residues: 28.1190 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 92 SER Chi-restraints excluded: chain D residue 111 THR 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 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 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.138087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110177 restraints weight = 23264.799| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.15 r_work: 0.3678 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1296 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= 0.149 Angle : 0.616 7.180 17250 Z= 0.357 Chirality : 0.042 0.342 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.977 157.996 3661 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.10 % Favored : 89.37 % Rotamer: Outliers : 10.44 % Allowed : 29.75 % Favored : 59.81 % 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: -0.20 (0.32), residues: 762 helix: 1.40 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 144 TYR 0.009 0.001 TYR G 134 PHE 0.013 0.002 PHE H 91 HIS 0.002 0.000 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (11971) covalent geometry : angle 0.61571 / 0.36 (17250) hydrogen bonds : bond 0.05528 / 3.78 ( 532) hydrogen bonds : angle 3.12370 / 2.20 ( 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 193 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.316 Fit side-chains REVERT: B 60 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7794 (m-40) REVERT: C 81 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8311 (tppt) REVERT: C 109 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 146 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5001 (pp) REVERT: D 104 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6847 (mptt) REVERT: D 124 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: D 155 MET cc_start: 0.7298 (tpp) cc_final: 0.6953 (tpt) REVERT: E 123 MET cc_start: 0.7567 (mtp) cc_final: 0.7128 (mtp) REVERT: G 140 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7607 (mt-10) REVERT: H 97 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: H 157 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7922 (mm-30) outliers start: 66 outliers final: 51 residues processed: 180 average time/residue: 0.1258 time to fit residues: 30.7283 Evaluate side-chains 177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 92 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR 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 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 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 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 149 VAL 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: 4.9990 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.138733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110834 restraints weight = 23199.523| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.18 r_work: 0.3689 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11971 Z= 0.141 Angle : 0.609 7.878 17250 Z= 0.353 Chirality : 0.041 0.343 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.970 157.827 3661 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.32 % Favored : 90.16 % Rotamer: Outliers : 10.28 % Allowed : 31.17 % Favored : 58.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.32), residues: 762 helix: 1.41 (0.25), residues: 473 sheet: None (None), residues: 0 loop : -2.87 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.008 0.001 TYR B 56 PHE 0.012 0.002 PHE C 98 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (11971) covalent geometry : angle 0.60923 / 0.35 (17250) hydrogen bonds : bond 0.05317 / 3.66 ( 532) hydrogen bonds : angle 3.08262 / 2.17 ( 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 187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 122 time to evaluate : 0.238 Fit side-chains REVERT: B 60 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: C 81 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8427 (tppt) REVERT: C 109 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 146 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.4981 (pp) REVERT: D 104 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6853 (mptt) REVERT: D 124 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6664 (mt0) REVERT: E 123 MET cc_start: 0.7546 (mtp) cc_final: 0.7113 (mtp) REVERT: G 140 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7544 (mt-10) REVERT: H 97 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: H 157 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7967 (mm-30) outliers start: 65 outliers final: 53 residues processed: 173 average time/residue: 0.1059 time to fit residues: 25.0011 Evaluate side-chains 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 121 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 60 ASN 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 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 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 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 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 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 ASN G 83 ASN H 124 GLN 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 = 0.138501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110758 restraints weight = 23114.361| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.13 r_work: 0.3687 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11971 Z= 0.145 Angle : 0.616 8.057 17250 Z= 0.355 Chirality : 0.042 0.345 1991 Planarity : 0.004 0.054 1272 Dihedral : 30.981 157.512 3659 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.71 % Favored : 89.76 % Rotamer: Outliers : 10.60 % Allowed : 30.54 % Favored : 58.86 % 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: -0.15 (0.32), residues: 762 helix: 1.41 (0.25), residues: 474 sheet: None (None), residues: 0 loop : -2.87 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.007 0.001 TYR F 56 PHE 0.017 0.002 PHE H 91 HIS 0.002 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (11971) covalent geometry : angle 0.61554 / 0.36 (17250) hydrogen bonds : bond 0.05358 / 3.67 ( 532) hydrogen bonds : angle 3.08990 / 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 191 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 124 time to evaluate : 0.204 Fit side-chains REVERT: B 60 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7821 (m-40) REVERT: C 81 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8360 (tppt) REVERT: C 109 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7660 (tm-30) REVERT: D 104 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6886 (mptt) REVERT: D 124 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6673 (mt0) REVERT: D 155 MET cc_start: 0.7078 (tpp) cc_final: 0.6836 (tpt) REVERT: D 162 LYS cc_start: 0.7782 (tptm) cc_final: 0.7551 (tptm) REVERT: E 123 MET cc_start: 0.7546 (mtp) cc_final: 0.7120 (mtp) REVERT: E 145 LYS cc_start: 0.7534 (ttpt) cc_final: 0.7320 (ttpt) REVERT: G 140 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7483 (mt-10) REVERT: H 97 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: H 157 GLU cc_start: 0.8202 (mm-30) cc_final: 0.8001 (mm-30) outliers start: 67 outliers final: 55 residues processed: 175 average time/residue: 0.1113 time to fit residues: 26.3207 Evaluate side-chains 182 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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 92 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR 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 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 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 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 149 VAL 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: 10.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN G 144 HIS H 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.139188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.111397 restraints weight = 22991.573| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.15 r_work: 0.3697 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11971 Z= 0.138 Angle : 0.616 8.334 17250 Z= 0.354 Chirality : 0.041 0.345 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.972 157.377 3659 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.79 % Favored : 90.68 % Rotamer: Outliers : 8.86 % Allowed : 32.28 % Favored : 58.86 % 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: -0.09 (0.33), residues: 762 helix: 1.46 (0.25), residues: 474 sheet: None (None), residues: 0 loop : -2.86 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.008 0.001 TYR F 56 PHE 0.012 0.002 PHE H 91 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (11971) covalent geometry : angle 0.61620 / 0.35 (17250) hydrogen bonds : bond 0.05220 / 3.59 ( 532) hydrogen bonds : angle 3.05341 / 2.14 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.243 Fit side-chains REVERT: C 81 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8365 (tppt) REVERT: C 109 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 146 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4949 (pp) REVERT: D 104 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6812 (mptt) REVERT: D 124 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6636 (mt0) REVERT: D 155 MET cc_start: 0.7084 (tpp) cc_final: 0.6809 (tpt) REVERT: E 123 MET cc_start: 0.7540 (mtp) cc_final: 0.7075 (mtp) REVERT: G 140 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7487 (mt-10) REVERT: H 97 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: H 157 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7953 (mm-30) outliers start: 56 outliers final: 50 residues processed: 168 average time/residue: 0.1277 time to fit residues: 28.7649 Evaluate side-chains 178 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 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 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 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 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.139863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.112339 restraints weight = 23158.761| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.10 r_work: 0.3714 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11971 Z= 0.136 Angle : 0.624 9.064 17250 Z= 0.357 Chirality : 0.041 0.342 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.939 157.267 3659 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.19 % Favored : 90.16 % Rotamer: Outliers : 8.39 % Allowed : 32.59 % Favored : 59.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.33), residues: 762 helix: 1.47 (0.25), residues: 475 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.007 0.001 TYR F 56 PHE 0.012 0.001 PHE H 91 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 0.62436 / 0.36 (17250) hydrogen bonds : bond 0.05100 / 3.52 ( 532) hydrogen bonds : angle 3.02151 / 2.12 ( 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 178 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.307 Fit side-chains REVERT: A 55 GLN cc_start: 0.7517 (mp10) cc_final: 0.7178 (mm-40) REVERT: C 81 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8467 (tppt) REVERT: C 109 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 146 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4907 (pp) REVERT: D 124 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: E 123 MET cc_start: 0.7435 (mtp) cc_final: 0.7038 (mtp) REVERT: G 140 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7374 (mt-10) REVERT: H 97 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7362 (tp30) outliers start: 53 outliers final: 44 residues processed: 166 average time/residue: 0.1136 time to fit residues: 25.6803 Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 GLU 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 97 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 149 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN G 83 ASN H 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.139586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.111773 restraints weight = 23103.613| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.16 r_work: 0.3705 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11971 Z= 0.140 Angle : 0.629 8.867 17250 Z= 0.358 Chirality : 0.041 0.342 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.945 157.003 3655 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.45 % Favored : 89.90 % Rotamer: Outliers : 8.54 % Allowed : 32.75 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.32), residues: 762 helix: 1.36 (0.25), residues: 481 sheet: None (None), residues: 0 loop : -2.88 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 132 TYR 0.009 0.001 TYR A 102 PHE 0.012 0.002 PHE H 91 HIS 0.003 0.000 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (11971) covalent geometry : angle 0.62885 / 0.36 (17250) hydrogen bonds : bond 0.05178 / 3.56 ( 532) hydrogen bonds : angle 3.06294 / 2.15 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.65 seconds wall clock time: 41 minutes 31.71 seconds (2491.71 seconds total)