Starting phenix.real_space_refine on Mon Jun 9 22:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua7_42053/06_2025/8ua7_42053.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.35, per 1000 atoms: 0.65 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: 2.90 Conformation dependent library (CDL) restraints added in 804.6 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: 5.68 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: 3.77 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1902 1.33 - 1.45: 4030 1.45 - 1.57: 5478 1.57 - 1.70: 517 1.70 - 1.82: 44 Bond restraints: 11971 Sorted by residual: bond pdb=" C LYS E 145 " pdb=" O LYS E 145 " ideal model delta sigma weight residual 1.236 1.312 -0.075 1.24e-02 6.50e+03 3.70e+01 bond pdb=" N LYS E 145 " pdb=" CA LYS E 145 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 9.92e+00 bond pdb=" N LEU D 117 " pdb=" CA LEU D 117 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.28e-02 6.10e+03 8.99e+00 bond pdb=" N ILE B 14 " pdb=" CA ILE B 14 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.80e+00 bond pdb=" N THR C 136 " pdb=" CA THR C 136 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 ... (remaining 11966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 17055 2.47 - 4.94: 176 4.94 - 7.41: 16 7.41 - 9.87: 2 9.87 - 12.34: 1 Bond angle restraints: 17250 Sorted by residual: angle pdb=" N ASN B 16 " pdb=" CA ASN B 16 " pdb=" C ASN B 16 " ideal model delta sigma weight residual 110.35 98.01 12.34 1.36e+00 5.41e-01 8.24e+01 angle pdb=" N ASP A 126 " pdb=" CA ASP A 126 " pdb=" C ASP A 126 " ideal model delta sigma weight residual 112.90 107.33 5.57 1.31e+00 5.83e-01 1.81e+01 angle pdb=" N SER C 152 " pdb=" CA SER C 152 " pdb=" C SER C 152 " ideal model delta sigma weight residual 107.73 112.51 -4.78 1.34e+00 5.57e-01 1.27e+01 angle pdb=" C ALA E 144 " pdb=" N LYS E 145 " pdb=" CA LYS E 145 " ideal model delta sigma weight residual 120.38 115.37 5.01 1.46e+00 4.69e-01 1.18e+01 angle pdb=" CA GLY C 154 " pdb=" C GLY C 154 " pdb=" O GLY C 154 " ideal model delta sigma weight residual 121.63 117.97 3.66 1.07e+00 8.73e-01 1.17e+01 ... (remaining 17245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 5225 34.21 - 68.43: 1299 68.43 - 102.64: 31 102.64 - 136.85: 1 136.85 - 171.06: 5 Dihedral angle restraints: 6561 sinusoidal: 4335 harmonic: 2226 Sorted by residual: dihedral pdb=" CD ARG G 75 " pdb=" NE ARG G 75 " pdb=" CZ ARG G 75 " pdb=" NH1 ARG G 75 " ideal model delta sinusoidal sigma weight residual 0.00 63.64 -63.64 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CA GLY A 70 " pdb=" C GLY A 70 " pdb=" N ARG A 71 " pdb=" CA ARG A 71 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG A 71 " pdb=" C ARG A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 6558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1734 0.052 - 0.105: 220 0.105 - 0.157: 30 0.157 - 0.209: 6 0.209 - 0.262: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA ASN B 16 " pdb=" N ASN B 16 " pdb=" C ASN B 16 " pdb=" CB ASN B 16 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE D 142 " pdb=" CA ILE D 142 " pdb=" CG1 ILE D 142 " pdb=" CG2 ILE D 142 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA ILE E 138 " pdb=" N ILE E 138 " pdb=" C ILE E 138 " pdb=" CB ILE E 138 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 1988 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 75 " -0.982 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG G 75 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG G 75 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 75 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 75 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 14 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ILE B 14 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 14 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 15 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 143 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C ALA D 143 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA D 143 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 144 " -0.014 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 325 2.66 - 3.22: 9772 3.22 - 3.78: 19471 3.78 - 4.34: 25040 4.34 - 4.90: 36539 Nonbonded interactions: 91147 Sorted by model distance: nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.099 2.496 nonbonded pdb=" NH1 ARG A 119 " pdb=" OD2 ASP A 126 " model vdw 2.184 3.120 nonbonded pdb=" NE2 HIS B 68 " pdb=" OD1 ASP D 130 " model vdw 2.205 3.120 nonbonded pdb=" O TYR G 134 " pdb=" N ASN G 138 " model vdw 2.205 3.120 nonbonded pdb=" O SER F 69 " pdb=" OG SER F 69 " model vdw 2.218 3.040 ... (remaining 91142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.980 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11971 Z= 0.241 Angle : 0.674 12.344 17250 Z= 0.413 Chirality : 0.037 0.262 1991 Planarity : 0.013 0.440 1272 Dihedral : 28.716 171.063 5117 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.63 % Favored : 88.98 % Rotamer: Outliers : 5.54 % Allowed : 33.07 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (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 HIS 0.002 0.000 HIS B 68 PHE 0.012 0.001 PHE C 98 TYR 0.009 0.001 TYR B 56 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.10131 ( 532) hydrogen bonds : angle 4.11468 ( 1353) covalent geometry : bond 0.00416 (11971) covalent geometry : angle 0.67443 (17250) *********************** 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 : 0.854 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: 0.3274 time to fit residues: 70.1598 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 : 0.878 ------------------------------------------------------------------------------- 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 84 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN G 83 ASN H 115 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.134757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107374 restraints weight = 23316.518| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.01 r_work: 0.3632 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11971 Z= 0.244 Angle : 0.652 6.325 17250 Z= 0.374 Chirality : 0.038 0.182 1991 Planarity : 0.005 0.050 1272 Dihedral : 30.845 154.484 3703 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 9.97 % Allowed : 31.65 % Favored : 58.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.31), residues: 762 helix: 0.70 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.16 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 120 PHE 0.021 0.003 PHE B 47 TYR 0.012 0.002 TYR G 134 ARG 0.004 0.001 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.06344 ( 532) hydrogen bonds : angle 3.44093 ( 1353) covalent geometry : bond 0.00549 (11971) covalent geometry : angle 0.65185 (17250) *********************** 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 195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 0.832 Fit side-chains REVERT: B 60 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7850 (m-40) REVERT: C 81 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8458 (tppt) REVERT: C 109 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7598 (tm-30) REVERT: D 104 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6914 (mptt) REVERT: D 124 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6669 (mt0) REVERT: E 52 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8248 (mmmt) REVERT: E 123 MET cc_start: 0.7789 (mtp) cc_final: 0.7483 (mtp) REVERT: G 140 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7712 (mt-10) REVERT: G 153 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.6029 (p-80) REVERT: H 132 ARG cc_start: 0.8086 (tmm-80) cc_final: 0.7709 (ttm170) outliers start: 63 outliers final: 46 residues processed: 180 average time/residue: 0.2883 time to fit residues: 68.6363 Evaluate side-chains 176 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 142 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.110895 restraints weight = 23315.856| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.17 r_work: 0.3690 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 0.048 11971 Z= 0.149 Angle : 0.577 7.889 17250 Z= 0.334 Chirality : 0.033 0.192 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.636 155.882 3677 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.53 % Favored : 90.81 % Rotamer: Outliers : 6.65 % Allowed : 33.86 % Favored : 59.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.32), residues: 762 helix: 1.35 (0.25), residues: 471 sheet: None (None), residues: 0 loop : -2.88 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 68 PHE 0.013 0.002 PHE F 47 TYR 0.008 0.001 TYR F 56 ARG 0.002 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 532) hydrogen bonds : angle 3.09754 ( 1353) covalent geometry : bond 0.00313 (11971) covalent geometry : angle 0.57688 (17250) *********************** 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 174 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.883 Fit side-chains REVERT: B 49 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8340 (mtmm) REVERT: C 81 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8449 (tppt) REVERT: C 109 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7650 (tm-30) REVERT: C 146 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.5024 (pp) REVERT: D 104 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6801 (mptt) REVERT: D 124 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6664 (mt0) REVERT: D 155 MET cc_start: 0.7125 (tpp) cc_final: 0.6838 (tpt) REVERT: D 158 LYS cc_start: 0.8164 (tppt) cc_final: 0.7945 (tptt) REVERT: E 52 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8224 (mmmt) REVERT: E 123 MET cc_start: 0.7588 (mtp) cc_final: 0.7302 (mtp) REVERT: G 140 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7454 (mt-10) REVERT: H 132 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7661 (ttm170) outliers start: 42 outliers final: 32 residues processed: 162 average time/residue: 0.3008 time to fit residues: 64.3213 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain E residue 46 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 105 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 130 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.110537 restraints weight = 23239.897| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.17 r_work: 0.3681 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11971 Z= 0.158 Angle : 0.575 8.092 17250 Z= 0.333 Chirality : 0.034 0.189 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.624 154.947 3661 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.58 % Favored : 89.90 % Rotamer: Outliers : 9.65 % Allowed : 31.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.32), residues: 762 helix: 1.37 (0.25), residues: 478 sheet: None (None), residues: 0 loop : -2.86 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 68 PHE 0.013 0.002 PHE H 91 TYR 0.008 0.001 TYR F 56 ARG 0.004 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 532) hydrogen bonds : angle 3.04476 ( 1353) covalent geometry : bond 0.00342 (11971) covalent geometry : angle 0.57537 (17250) *********************** 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 187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.899 Fit side-chains REVERT: B 49 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8433 (mtmm) REVERT: C 81 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8445 (tppt) REVERT: C 109 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: C 143 MET cc_start: 0.8614 (tpt) cc_final: 0.8374 (tpp) REVERT: D 104 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6827 (mptt) REVERT: D 124 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6666 (mt0) REVERT: D 155 MET cc_start: 0.7239 (tpp) cc_final: 0.6992 (tpt) REVERT: D 158 LYS cc_start: 0.8172 (tppt) cc_final: 0.7929 (tptt) REVERT: E 52 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8217 (mmmt) REVERT: E 123 MET cc_start: 0.7585 (mtp) cc_final: 0.7243 (mtp) REVERT: F 71 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6923 (mtp180) REVERT: G 140 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7535 (mt-10) REVERT: H 124 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6235 (pt0) REVERT: H 132 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7664 (ttm170) outliers start: 61 outliers final: 46 residues processed: 169 average time/residue: 0.2964 time to fit residues: 66.2995 Evaluate side-chains 174 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 79 LEU 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 161 LEU Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 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 106 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU 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 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE 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 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.138324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110796 restraints weight = 23017.972| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.10 r_work: 0.3689 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11971 Z= 0.156 Angle : 0.572 6.773 17250 Z= 0.331 Chirality : 0.033 0.134 1991 Planarity : 0.004 0.057 1272 Dihedral : 30.586 154.368 3659 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.32 % Favored : 90.16 % Rotamer: Outliers : 9.34 % Allowed : 31.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 762 helix: 1.40 (0.25), residues: 478 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 68 PHE 0.011 0.001 PHE C 98 TYR 0.008 0.001 TYR F 56 ARG 0.007 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 532) hydrogen bonds : angle 3.03518 ( 1353) covalent geometry : bond 0.00337 (11971) covalent geometry : angle 0.57157 (17250) *********************** 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 188 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 0.889 Fit side-chains REVERT: B 49 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8419 (mtmm) REVERT: C 81 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8437 (tppt) REVERT: C 109 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: C 146 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4866 (pp) REVERT: D 124 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6695 (mt0) REVERT: D 158 LYS cc_start: 0.8185 (tppt) cc_final: 0.7937 (tptt) REVERT: E 52 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8233 (mmmt) REVERT: E 123 MET cc_start: 0.7493 (mtp) cc_final: 0.7127 (mtp) REVERT: G 59 ASN cc_start: 0.7366 (m-40) cc_final: 0.7133 (t0) REVERT: G 140 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7422 (mt-10) REVERT: H 124 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6203 (pt0) REVERT: H 132 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7668 (ttm170) outliers start: 59 outliers final: 52 residues processed: 171 average time/residue: 0.2938 time to fit residues: 66.3777 Evaluate side-chains 180 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 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 161 LEU 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 106 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106452 restraints weight = 23515.612| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.15 r_work: 0.3615 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11971 Z= 0.238 Angle : 0.655 7.479 17250 Z= 0.373 Chirality : 0.037 0.140 1991 Planarity : 0.005 0.053 1272 Dihedral : 30.855 151.955 3653 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.10 % Favored : 89.50 % Rotamer: Outliers : 11.55 % Allowed : 30.38 % Favored : 58.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.32), residues: 762 helix: 0.90 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -2.98 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 120 PHE 0.020 0.002 PHE H 91 TYR 0.011 0.002 TYR B 56 ARG 0.003 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.06182 ( 532) hydrogen bonds : angle 3.30238 ( 1353) covalent geometry : bond 0.00537 (11971) covalent geometry : angle 0.65502 (17250) *********************** 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 195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 122 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: B 60 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: C 81 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8232 (tppt) REVERT: C 109 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: D 104 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6902 (mptt) REVERT: D 124 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: D 158 LYS cc_start: 0.8193 (tppt) cc_final: 0.7976 (tptt) REVERT: E 52 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8215 (mmmt) REVERT: E 123 MET cc_start: 0.7653 (mtp) cc_final: 0.7295 (mtp) REVERT: F 71 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7098 (mtm-85) REVERT: G 140 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7670 (mt-10) REVERT: G 153 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5909 (p-80) REVERT: H 124 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: H 132 ARG cc_start: 0.8079 (tmm-80) cc_final: 0.7687 (ttm170) outliers start: 73 outliers final: 53 residues processed: 177 average time/residue: 0.2836 time to fit residues: 66.8118 Evaluate side-chains 180 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 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 161 LEU Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE 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 43 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.137028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109336 restraints weight = 23368.030| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.15 r_work: 0.3663 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11971 Z= 0.167 Angle : 0.608 7.088 17250 Z= 0.348 Chirality : 0.034 0.136 1991 Planarity : 0.004 0.054 1272 Dihedral : 30.708 152.082 3653 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.84 % Favored : 89.63 % Rotamer: Outliers : 10.92 % Allowed : 31.33 % Favored : 57.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.32), residues: 762 helix: 1.10 (0.25), residues: 491 sheet: None (None), residues: 0 loop : -2.96 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 68 PHE 0.016 0.002 PHE H 91 TYR 0.010 0.001 TYR F 56 ARG 0.003 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 532) hydrogen bonds : angle 3.09969 ( 1353) covalent geometry : bond 0.00364 (11971) covalent geometry : angle 0.60805 (17250) *********************** 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 199 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 130 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 81 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8245 (tppt) REVERT: C 109 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: D 104 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6781 (mptt) REVERT: D 124 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6692 (mt0) REVERT: D 158 LYS cc_start: 0.8127 (tppt) cc_final: 0.7914 (tptt) REVERT: E 52 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8192 (mmmt) REVERT: E 123 MET cc_start: 0.7505 (mtp) cc_final: 0.7105 (mtp) REVERT: G 140 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7564 (mt-10) REVERT: G 153 HIS cc_start: 0.5999 (OUTLIER) cc_final: 0.5785 (p-80) REVERT: H 124 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: H 132 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7651 (ttm170) outliers start: 69 outliers final: 54 residues processed: 178 average time/residue: 0.2844 time to fit residues: 67.7027 Evaluate side-chains 183 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 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 G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 142 ILE 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 17 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109951 restraints weight = 23348.281| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.14 r_work: 0.3671 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11971 Z= 0.164 Angle : 0.608 7.445 17250 Z= 0.347 Chirality : 0.034 0.146 1991 Planarity : 0.004 0.056 1272 Dihedral : 30.664 150.931 3653 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.10 % Favored : 89.37 % Rotamer: Outliers : 10.13 % Allowed : 32.28 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.32), residues: 762 helix: 1.31 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -2.98 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 68 PHE 0.011 0.002 PHE C 98 TYR 0.009 0.001 TYR F 56 ARG 0.002 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 532) hydrogen bonds : angle 3.06872 ( 1353) covalent geometry : bond 0.00357 (11971) covalent geometry : angle 0.60822 (17250) *********************** 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 188 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7096 (ttp-170) REVERT: C 81 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8459 (tppt) REVERT: C 109 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: D 104 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6869 (mptt) REVERT: D 124 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6647 (mt0) REVERT: E 123 MET cc_start: 0.7491 (mtp) cc_final: 0.7107 (mtp) REVERT: G 140 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7535 (mt-10) REVERT: G 153 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.5715 (p-80) REVERT: H 124 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6271 (pt0) REVERT: H 132 ARG cc_start: 0.7992 (tmm-80) cc_final: 0.7666 (ttm170) outliers start: 64 outliers final: 52 residues processed: 168 average time/residue: 0.2880 time to fit residues: 64.0922 Evaluate side-chains 177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 21 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 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 G residue 153 HIS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.0010 chunk 53 optimal weight: 0.0020 chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN G 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.140638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.113171 restraints weight = 23094.922| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.19 r_work: 0.3724 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11971 Z= 0.144 Angle : 0.594 8.050 17250 Z= 0.339 Chirality : 0.033 0.155 1991 Planarity : 0.004 0.060 1272 Dihedral : 30.529 149.856 3649 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.53 % Favored : 90.94 % Rotamer: Outliers : 6.01 % Allowed : 36.39 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.33), residues: 762 helix: 1.48 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.05 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS B 68 PHE 0.022 0.001 PHE F 47 TYR 0.009 0.001 TYR F 56 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 532) hydrogen bonds : angle 2.97318 ( 1353) covalent geometry : bond 0.00305 (11971) covalent geometry : angle 0.59384 (17250) *********************** 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 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7439 (mp10) cc_final: 0.7227 (mm-40) REVERT: B 32 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8244 (ttm-80) REVERT: C 81 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8407 (tppt) REVERT: C 109 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 123 MET cc_start: 0.7377 (mtp) cc_final: 0.6979 (mtp) REVERT: G 140 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7489 (mt-10) REVERT: H 96 MET cc_start: 0.8209 (mmm) cc_final: 0.7838 (tpp) REVERT: H 124 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6354 (pt0) REVERT: H 132 ARG cc_start: 0.7978 (tmm-80) cc_final: 0.7682 (ttm170) outliers start: 38 outliers final: 29 residues processed: 159 average time/residue: 0.2941 time to fit residues: 62.1455 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 21 ILE 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 153 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 92 VAL 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 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 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 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 18 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 ASN G 129 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 = 0.137892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110110 restraints weight = 23129.013| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.12 r_work: 0.3676 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11971 Z= 0.176 Angle : 0.631 9.991 17250 Z= 0.356 Chirality : 0.034 0.179 1991 Planarity : 0.004 0.059 1272 Dihedral : 30.607 147.073 3647 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 5.54 % Allowed : 37.03 % Favored : 57.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.33), residues: 762 helix: 1.43 (0.25), residues: 477 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 68 PHE 0.017 0.002 PHE F 47 TYR 0.009 0.001 TYR F 56 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 532) hydrogen bonds : angle 3.07243 ( 1353) covalent geometry : bond 0.00388 (11971) covalent geometry : angle 0.63125 (17250) ********************** 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 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7105 (ttp-170) REVERT: C 81 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8389 (tppt) REVERT: C 109 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7716 (tm-30) REVERT: E 123 MET cc_start: 0.7497 (mtp) cc_final: 0.7069 (mtp) REVERT: G 140 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7566 (mt-10) REVERT: H 96 MET cc_start: 0.8287 (mmm) cc_final: 0.7923 (tpp) REVERT: H 124 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6420 (pt0) outliers start: 35 outliers final: 30 residues processed: 149 average time/residue: 0.2986 time to fit residues: 58.7163 Evaluate side-chains 151 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE 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 80 ARG 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 115 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 92 VAL 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 G residue 83 ASN Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 138 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 HIS Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 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 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.137941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110202 restraints weight = 23066.139| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.12 r_work: 0.3677 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11971 Z= 0.182 Angle : 0.855 59.197 17250 Z= 0.503 Chirality : 0.042 1.101 1991 Planarity : 0.005 0.072 1272 Dihedral : 30.611 147.072 3647 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 5.70 % Allowed : 36.71 % Favored : 57.59 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.33), residues: 762 helix: 1.43 (0.25), residues: 477 sheet: None (None), residues: 0 loop : -2.92 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 68 PHE 0.015 0.002 PHE F 47 TYR 0.009 0.001 TYR F 56 ARG 0.008 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 532) hydrogen bonds : angle 3.07187 ( 1353) covalent geometry : bond 0.00394 (11971) covalent geometry : angle 0.85456 (17250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5315.49 seconds wall clock time: 91 minutes 47.12 seconds (5507.12 seconds total)