Starting phenix.real_space_refine on Fri Feb 6 15:24:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9phb_71644/02_2026/9phb_71644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9phb_71644/02_2026/9phb_71644.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/9phb_71644/02_2026/9phb_71644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9phb_71644/02_2026/9phb_71644.map" model { file = "/net/cci-nas-00/data/ceres_data/9phb_71644/02_2026/9phb_71644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9phb_71644/02_2026/9phb_71644.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 8330 2.51 5 N 1990 2.21 5 O 2420 1.98 5 H 12760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "I" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "E" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "D" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "F" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "H" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "J" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "C" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2556 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Time building chain proxies: 3.51, per 1000 atoms: 0.14 Number of scatterers: 25560 At special positions: 0 Unit cell: (157.594, 88.5248, 148.838, 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 60 16.00 O 2420 8.00 N 1990 7.00 C 8330 6.00 H 12760 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 713.8 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 52.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 139 Processing helix chain 'G' and resid 141 through 143 No H-bonds generated for 'chain 'G' and resid 141 through 143' Processing helix chain 'G' and resid 160 through 172 removed outlier: 3.767A pdb=" N LEU G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 200 Processing helix chain 'G' and resid 230 through 246 Processing helix chain 'G' and resid 250 through 266 removed outlier: 4.093A pdb=" N ARG G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 139 removed outlier: 3.624A pdb=" N GLY I 139 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.824A pdb=" N LEU I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY I 172 " --> pdb=" O HIS I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 200 Processing helix chain 'I' and resid 230 through 246 Processing helix chain 'I' and resid 250 through 266 removed outlier: 3.881A pdb=" N ARG I 256 " --> pdb=" O LYS I 252 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 removed outlier: 3.574A pdb=" N GLY B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.507A pdb=" N HIS B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.634A pdb=" N LEU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 139 removed outlier: 3.622A pdb=" N GLY E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.606A pdb=" N LYS E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 230 through 246 Processing helix chain 'E' and resid 250 through 266 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 124 through 139 removed outlier: 3.550A pdb=" N GLY D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 172 removed outlier: 3.891A pdb=" N LEU D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 230 through 246 Processing helix chain 'D' and resid 250 through 266 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.519A pdb=" N HIS A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.760A pdb=" N ASN A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 246 Processing helix chain 'A' and resid 250 through 266 Processing helix chain 'F' and resid 124 through 139 removed outlier: 3.655A pdb=" N GLY F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 172 removed outlier: 3.599A pdb=" N GLY F 172 " --> pdb=" O HIS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 230 through 246 Processing helix chain 'F' and resid 250 through 266 Processing helix chain 'H' and resid 125 through 139 removed outlier: 3.537A pdb=" N GLY H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'H' and resid 186 through 200 removed outlier: 3.572A pdb=" N LEU H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 246 Processing helix chain 'H' and resid 250 through 266 Processing helix chain 'J' and resid 121 through 123 No H-bonds generated for 'chain 'J' and resid 121 through 123' Processing helix chain 'J' and resid 124 through 139 removed outlier: 3.514A pdb=" N GLY J 139 " --> pdb=" O LEU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 172 removed outlier: 3.554A pdb=" N HIS J 168 " --> pdb=" O TYR J 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 171 " --> pdb=" O LYS J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 186 removed outlier: 4.036A pdb=" N SER J 186 " --> pdb=" O TYR J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 200 removed outlier: 3.555A pdb=" N ASN J 199 " --> pdb=" O ALA J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 246 Processing helix chain 'J' and resid 250 through 266 removed outlier: 3.840A pdb=" N ARG J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA J 259 " --> pdb=" O GLU J 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 139 removed outlier: 3.537A pdb=" N GLY C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.831A pdb=" N LEU C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.877A pdb=" N ARG C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 145 through 146 removed outlier: 6.899A pdb=" N ILE G 116 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 116 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.848A pdb=" N ILE B 116 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE B 117 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET B 178 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER B 119 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE B 206 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR B 177 " --> pdb=" O PHE B 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 145 through 146 removed outlier: 6.813A pdb=" N ILE E 116 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 116 through 117 removed outlier: 7.397A pdb=" N PHE D 117 " --> pdb=" O PHE D 176 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 178 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 175 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE D 206 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR D 177 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N PHE D 226 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR D 205 " --> pdb=" O PHE D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 6.496A pdb=" N PHE A 117 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET A 178 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER A 119 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE A 206 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR A 177 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 116 through 119 removed outlier: 6.629A pdb=" N PHE F 117 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET F 178 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER F 119 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE F 206 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR F 177 " --> pdb=" O PHE F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'J' and resid 116 through 119 removed outlier: 3.516A pdb=" N PHE J 226 " --> pdb=" O THR J 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 146 removed outlier: 7.098A pdb=" N ILE C 116 " --> pdb=" O ILE C 146 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12730 1.03 - 1.23: 36 1.23 - 1.42: 5534 1.42 - 1.62: 7460 1.62 - 1.81: 90 Bond restraints: 25850 Sorted by residual: bond pdb=" N GLU F 111 " pdb=" CA GLU F 111 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N GLU A 111 " pdb=" CA GLU A 111 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N GLU H 111 " pdb=" CA GLU H 111 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N GLU B 111 " pdb=" CA GLU B 111 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU E 111 " pdb=" CA GLU E 111 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 25845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 44868 1.16 - 2.32: 1882 2.32 - 3.48: 82 3.48 - 4.65: 27 4.65 - 5.81: 1 Bond angle restraints: 46860 Sorted by residual: angle pdb=" N GLU H 230 " pdb=" CA GLU H 230 " pdb=" C GLU H 230 " ideal model delta sigma weight residual 108.22 110.70 -2.48 9.00e-01 1.23e+00 7.56e+00 angle pdb=" N ILE G 118 " pdb=" CA ILE G 118 " pdb=" C ILE G 118 " ideal model delta sigma weight residual 106.55 110.10 -3.55 1.45e+00 4.76e-01 6.00e+00 angle pdb=" N ILE G 146 " pdb=" CA ILE G 146 " pdb=" C ILE G 146 " ideal model delta sigma weight residual 106.21 108.75 -2.54 1.07e+00 8.73e-01 5.62e+00 angle pdb=" N GLU I 230 " pdb=" CA GLU I 230 " pdb=" C GLU I 230 " ideal model delta sigma weight residual 108.13 110.12 -1.99 9.00e-01 1.23e+00 4.87e+00 angle pdb=" N VAL C 218 " pdb=" CA VAL C 218 " pdb=" C VAL C 218 " ideal model delta sigma weight residual 111.88 109.59 2.29 1.06e+00 8.90e-01 4.66e+00 ... (remaining 46855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10649 17.87 - 35.73: 1025 35.73 - 53.60: 336 53.60 - 71.47: 90 71.47 - 89.33: 10 Dihedral angle restraints: 12110 sinusoidal: 6440 harmonic: 5670 Sorted by residual: dihedral pdb=" CB GLU F 111 " pdb=" CG GLU F 111 " pdb=" CD GLU F 111 " pdb=" OE1 GLU F 111 " ideal model delta sinusoidal sigma weight residual 0.00 -89.33 89.33 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP C 220 " pdb=" CB ASP C 220 " pdb=" CG ASP C 220 " pdb=" OD1 ASP C 220 " ideal model delta sinusoidal sigma weight residual -30.00 -84.25 54.25 1 2.00e+01 2.50e-03 9.98e+00 dihedral pdb=" N GLU G 111 " pdb=" CA GLU G 111 " pdb=" CB GLU G 111 " pdb=" CG GLU G 111 " ideal model delta sinusoidal sigma weight residual -60.00 -119.65 59.65 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 12107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1124 0.027 - 0.055: 492 0.055 - 0.082: 152 0.082 - 0.109: 91 0.109 - 0.137: 31 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CA ILE H 155 " pdb=" N ILE H 155 " pdb=" C ILE H 155 " pdb=" CB ILE H 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 155 " pdb=" N ILE B 155 " pdb=" C ILE B 155 " pdb=" CB ILE B 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE F 155 " pdb=" N ILE F 155 " pdb=" C ILE F 155 " pdb=" CB ILE F 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1887 not shown) Planarity restraints: 3710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 246 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ASP D 246 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP D 246 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 247 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 185 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" CG ASP F 185 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP F 185 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 185 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 130 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C ALA A 130 " -0.022 2.00e-02 2.50e+03 pdb=" O ALA A 130 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE A 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 3707 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1699 2.21 - 2.81: 53069 2.81 - 3.40: 65158 3.40 - 4.00: 86371 4.00 - 4.60: 136136 Nonbonded interactions: 342433 Sorted by model distance: nonbonded pdb=" O LYS A 258 " pdb="HD21 ASN A 262 " model vdw 1.611 2.450 nonbonded pdb=" OG SER B 150 " pdb=" HD1 HIS B 153 " model vdw 1.619 2.450 nonbonded pdb=" OG SER J 150 " pdb=" HD1 HIS J 153 " model vdw 1.643 2.450 nonbonded pdb=" O LYS F 258 " pdb="HD21 ASN F 262 " model vdw 1.646 2.450 nonbonded pdb=" H GLU E 230 " pdb=" OD2 ASP E 233 " model vdw 1.651 2.450 ... (remaining 342428 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.003 0.033 13090 Z= 0.129 Angle : 0.477 5.808 17600 Z= 0.282 Chirality : 0.039 0.137 1890 Planarity : 0.003 0.041 2200 Dihedral : 17.424 89.335 4910 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.14 % Allowed : 19.58 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1540 helix: 2.18 (0.19), residues: 710 sheet: -4.14 (0.40), residues: 120 loop : -1.04 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 243 TYR 0.013 0.001 TYR C 164 PHE 0.015 0.001 PHE B 261 TRP 0.007 0.001 TRP A 254 HIS 0.004 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00258 (13090) covalent geometry : angle 0.47707 (17600) hydrogen bonds : bond 0.15931 ( 603) hydrogen bonds : angle 6.27364 ( 1785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 255 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6436 (mm-30) REVERT: B 114 LYS cc_start: 0.6759 (mmtt) cc_final: 0.6489 (mmmt) REVERT: B 243 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7386 (mtp180) REVERT: D 255 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6276 (mm-30) REVERT: A 178 MET cc_start: 0.8625 (mmm) cc_final: 0.8309 (mmm) outliers start: 2 outliers final: 2 residues processed: 211 average time/residue: 0.2279 time to fit residues: 69.5650 Evaluate side-chains 165 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain J residue 174 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118789 restraints weight = 43694.069| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.44 r_work: 0.3502 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13090 Z= 0.224 Angle : 0.524 4.742 17600 Z= 0.295 Chirality : 0.042 0.148 1890 Planarity : 0.003 0.025 2200 Dihedral : 4.287 53.729 1673 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.70 % Allowed : 19.02 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1540 helix: 2.06 (0.18), residues: 740 sheet: -3.99 (0.31), residues: 170 loop : -1.03 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 243 TYR 0.015 0.002 TYR A 147 PHE 0.013 0.002 PHE D 226 TRP 0.007 0.002 TRP B 254 HIS 0.007 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00539 (13090) covalent geometry : angle 0.52415 (17600) hydrogen bonds : bond 0.05947 ( 603) hydrogen bonds : angle 5.02042 ( 1785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 GLU cc_start: 0.5798 (mm-30) cc_final: 0.5524 (mm-30) REVERT: E 125 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7114 (mtmm) REVERT: A 178 MET cc_start: 0.8597 (mmm) cc_final: 0.8265 (mmm) REVERT: A 185 ASP cc_start: 0.8554 (t0) cc_final: 0.8327 (t0) REVERT: H 174 TYR cc_start: 0.7451 (m-80) cc_final: 0.7232 (m-80) REVERT: H 255 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6529 (mm-30) REVERT: J 255 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6384 (mm-30) REVERT: J 262 ASN cc_start: 0.8427 (m110) cc_final: 0.8115 (m110) REVERT: C 255 GLU cc_start: 0.5830 (pt0) cc_final: 0.5107 (pt0) outliers start: 10 outliers final: 6 residues processed: 179 average time/residue: 0.2536 time to fit residues: 65.3968 Evaluate side-chains 153 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 203 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118501 restraints weight = 43419.335| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.51 r_work: 0.3492 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13090 Z= 0.192 Angle : 0.495 4.065 17600 Z= 0.277 Chirality : 0.041 0.147 1890 Planarity : 0.003 0.029 2200 Dihedral : 4.284 52.705 1672 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.98 % Allowed : 18.25 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1540 helix: 2.19 (0.18), residues: 740 sheet: -4.00 (0.31), residues: 170 loop : -1.12 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 243 TYR 0.012 0.002 TYR C 164 PHE 0.011 0.001 PHE D 226 TRP 0.006 0.001 TRP B 254 HIS 0.006 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00459 (13090) covalent geometry : angle 0.49519 (17600) hydrogen bonds : bond 0.05289 ( 603) hydrogen bonds : angle 4.74576 ( 1785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 GLU cc_start: 0.5930 (mm-30) cc_final: 0.5615 (mm-30) REVERT: E 125 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7094 (mtmm) REVERT: A 185 ASP cc_start: 0.8581 (t0) cc_final: 0.8244 (t0) REVERT: H 135 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (mt) REVERT: H 174 TYR cc_start: 0.7539 (m-80) cc_final: 0.7209 (m-80) REVERT: H 255 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6335 (mm-30) REVERT: J 255 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6325 (mm-30) REVERT: J 262 ASN cc_start: 0.8467 (m110) cc_final: 0.8035 (m110) outliers start: 14 outliers final: 7 residues processed: 176 average time/residue: 0.2503 time to fit residues: 64.6467 Evaluate side-chains 156 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120216 restraints weight = 42915.570| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.49 r_work: 0.3337 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13090 Z= 0.140 Angle : 0.460 3.932 17600 Z= 0.256 Chirality : 0.040 0.142 1890 Planarity : 0.003 0.028 2200 Dihedral : 4.142 52.443 1672 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.26 % Allowed : 18.53 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1540 helix: 2.49 (0.18), residues: 740 sheet: -3.97 (0.33), residues: 150 loop : -1.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 243 TYR 0.011 0.002 TYR C 164 PHE 0.008 0.001 PHE D 226 TRP 0.006 0.001 TRP E 197 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00328 (13090) covalent geometry : angle 0.45993 (17600) hydrogen bonds : bond 0.04542 ( 603) hydrogen bonds : angle 4.50451 ( 1785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 255 GLU cc_start: 0.5988 (mm-30) cc_final: 0.5646 (mm-30) REVERT: E 125 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7105 (mtmm) REVERT: A 178 MET cc_start: 0.8775 (mmm) cc_final: 0.7644 (mmm) REVERT: A 185 ASP cc_start: 0.8479 (t0) cc_final: 0.8175 (t0) REVERT: H 135 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8412 (mt) REVERT: H 174 TYR cc_start: 0.7563 (m-80) cc_final: 0.7132 (m-80) REVERT: H 255 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6374 (mm-30) REVERT: J 255 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6325 (mm-30) REVERT: J 262 ASN cc_start: 0.8497 (m110) cc_final: 0.8113 (m110) outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.2310 time to fit residues: 61.7567 Evaluate side-chains 159 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.117851 restraints weight = 43407.602| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.50 r_work: 0.3304 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13090 Z= 0.218 Angle : 0.512 4.041 17600 Z= 0.288 Chirality : 0.042 0.148 1890 Planarity : 0.003 0.029 2200 Dihedral : 4.320 51.818 1672 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.40 % Allowed : 18.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1540 helix: 2.18 (0.18), residues: 740 sheet: -4.03 (0.33), residues: 150 loop : -1.27 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 243 TYR 0.013 0.002 TYR A 147 PHE 0.013 0.002 PHE D 226 TRP 0.007 0.001 TRP E 197 HIS 0.006 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00526 (13090) covalent geometry : angle 0.51250 (17600) hydrogen bonds : bond 0.05336 ( 603) hydrogen bonds : angle 4.74016 ( 1785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 255 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5729 (mm-30) REVERT: E 125 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7026 (mtmm) REVERT: A 178 MET cc_start: 0.8790 (mmm) cc_final: 0.7635 (mmm) REVERT: A 185 ASP cc_start: 0.8537 (t0) cc_final: 0.8115 (t0) REVERT: F 135 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (mt) REVERT: F 185 ASP cc_start: 0.8577 (t0) cc_final: 0.8353 (t0) REVERT: H 135 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8448 (mt) REVERT: H 174 TYR cc_start: 0.7718 (m-80) cc_final: 0.7230 (m-80) REVERT: H 255 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6350 (mm-30) REVERT: J 255 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6453 (mm-30) REVERT: J 262 ASN cc_start: 0.8536 (m110) cc_final: 0.8162 (m110) REVERT: C 255 GLU cc_start: 0.5948 (pt0) cc_final: 0.5232 (pt0) outliers start: 20 outliers final: 13 residues processed: 171 average time/residue: 0.2378 time to fit residues: 58.7330 Evaluate side-chains 163 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118987 restraints weight = 43283.545| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.51 r_work: 0.3320 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13090 Z= 0.174 Angle : 0.486 4.002 17600 Z= 0.272 Chirality : 0.041 0.145 1890 Planarity : 0.003 0.028 2200 Dihedral : 4.257 51.381 1672 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.33 % Allowed : 18.88 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1540 helix: 2.33 (0.18), residues: 740 sheet: -4.04 (0.32), residues: 150 loop : -1.23 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 243 TYR 0.011 0.002 TYR C 164 PHE 0.009 0.001 PHE D 226 TRP 0.007 0.001 TRP E 197 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00415 (13090) covalent geometry : angle 0.48598 (17600) hydrogen bonds : bond 0.04861 ( 603) hydrogen bonds : angle 4.60134 ( 1785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8523 (mt) REVERT: B 255 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5710 (mm-30) REVERT: E 125 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7041 (mtmm) REVERT: E 230 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 178 MET cc_start: 0.8789 (mmm) cc_final: 0.7614 (mmm) REVERT: F 185 ASP cc_start: 0.8504 (t0) cc_final: 0.8285 (t0) REVERT: H 135 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8441 (mt) REVERT: H 174 TYR cc_start: 0.7690 (m-80) cc_final: 0.7207 (m-80) REVERT: H 255 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6341 (mm-30) REVERT: J 255 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6371 (mm-30) REVERT: J 262 ASN cc_start: 0.8567 (m110) cc_final: 0.8187 (m110) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.2293 time to fit residues: 57.4912 Evaluate side-chains 161 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119230 restraints weight = 43186.725| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.49 r_work: 0.3327 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13090 Z= 0.163 Angle : 0.477 3.898 17600 Z= 0.267 Chirality : 0.040 0.144 1890 Planarity : 0.003 0.028 2200 Dihedral : 4.200 51.022 1672 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.47 % Allowed : 18.60 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1540 helix: 2.41 (0.18), residues: 740 sheet: -4.05 (0.32), residues: 150 loop : -1.20 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 243 TYR 0.011 0.002 TYR C 164 PHE 0.009 0.001 PHE D 226 TRP 0.008 0.001 TRP E 197 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00389 (13090) covalent geometry : angle 0.47698 (17600) hydrogen bonds : bond 0.04674 ( 603) hydrogen bonds : angle 4.56187 ( 1785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 255 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5741 (mm-30) REVERT: E 125 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7011 (mtmm) REVERT: E 230 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 178 MET cc_start: 0.8791 (mmm) cc_final: 0.7602 (mmm) REVERT: A 185 ASP cc_start: 0.8373 (t0) cc_final: 0.8076 (t0) REVERT: F 185 ASP cc_start: 0.8528 (t0) cc_final: 0.8297 (t0) REVERT: H 135 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (mt) REVERT: H 174 TYR cc_start: 0.7723 (m-80) cc_final: 0.7185 (m-80) REVERT: H 255 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6384 (mm-30) REVERT: J 255 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6347 (mm-30) REVERT: J 262 ASN cc_start: 0.8567 (m110) cc_final: 0.8199 (m110) outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 0.2170 time to fit residues: 56.6202 Evaluate side-chains 171 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119351 restraints weight = 43131.225| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.42 r_work: 0.3330 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13090 Z= 0.173 Angle : 0.485 4.308 17600 Z= 0.271 Chirality : 0.041 0.145 1890 Planarity : 0.003 0.028 2200 Dihedral : 4.213 50.643 1672 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.40 % Allowed : 19.23 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1540 helix: 2.37 (0.18), residues: 740 sheet: -4.06 (0.32), residues: 150 loop : -1.21 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 256 TYR 0.011 0.002 TYR C 164 PHE 0.010 0.001 PHE D 226 TRP 0.008 0.001 TRP E 197 HIS 0.004 0.001 HIS J 153 Details of bonding type rmsd covalent geometry : bond 0.00415 (13090) covalent geometry : angle 0.48478 (17600) hydrogen bonds : bond 0.04753 ( 603) hydrogen bonds : angle 4.59333 ( 1785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (mt) REVERT: B 255 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5687 (mm-30) REVERT: E 125 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7068 (mtmm) REVERT: E 230 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 178 MET cc_start: 0.8803 (mmm) cc_final: 0.7589 (mmm) REVERT: F 185 ASP cc_start: 0.8538 (t0) cc_final: 0.8291 (t0) REVERT: H 135 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8443 (mt) REVERT: H 174 TYR cc_start: 0.7753 (m-80) cc_final: 0.7234 (m-80) REVERT: H 255 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6337 (mm-30) REVERT: J 255 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6292 (mm-30) REVERT: J 262 ASN cc_start: 0.8594 (m110) cc_final: 0.8243 (m110) outliers start: 20 outliers final: 14 residues processed: 174 average time/residue: 0.2260 time to fit residues: 58.8685 Evaluate side-chains 170 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.130629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118045 restraints weight = 43572.513| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.49 r_work: 0.3306 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13090 Z= 0.205 Angle : 0.510 4.327 17600 Z= 0.286 Chirality : 0.041 0.146 1890 Planarity : 0.003 0.028 2200 Dihedral : 4.300 50.121 1672 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.40 % Allowed : 19.23 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1540 helix: 2.19 (0.18), residues: 740 sheet: -4.09 (0.32), residues: 150 loop : -1.30 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 256 TYR 0.011 0.002 TYR C 164 PHE 0.011 0.001 PHE D 226 TRP 0.009 0.001 TRP E 197 HIS 0.005 0.001 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00494 (13090) covalent geometry : angle 0.51019 (17600) hydrogen bonds : bond 0.05104 ( 603) hydrogen bonds : angle 4.70256 ( 1785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8538 (mt) REVERT: B 255 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5714 (mm-30) REVERT: E 125 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7085 (mtmm) REVERT: E 230 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 178 MET cc_start: 0.8816 (mmm) cc_final: 0.7624 (mmm) REVERT: F 185 ASP cc_start: 0.8564 (t0) cc_final: 0.8289 (t0) REVERT: H 135 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8450 (mt) REVERT: H 174 TYR cc_start: 0.7709 (m-80) cc_final: 0.7140 (m-80) REVERT: H 255 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6356 (mm-30) REVERT: J 255 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6312 (mm-30) REVERT: J 262 ASN cc_start: 0.8601 (m110) cc_final: 0.8261 (m110) REVERT: C 255 GLU cc_start: 0.5847 (pt0) cc_final: 0.5215 (pt0) outliers start: 20 outliers final: 15 residues processed: 169 average time/residue: 0.2393 time to fit residues: 60.4967 Evaluate side-chains 167 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120199 restraints weight = 43076.833| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.49 r_work: 0.3336 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13090 Z= 0.139 Angle : 0.468 4.789 17600 Z= 0.262 Chirality : 0.040 0.143 1890 Planarity : 0.003 0.029 2200 Dihedral : 4.157 50.174 1672 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.47 % Allowed : 19.23 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1540 helix: 2.53 (0.18), residues: 740 sheet: -4.02 (0.32), residues: 150 loop : -1.16 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 243 TYR 0.013 0.002 TYR G 177 PHE 0.008 0.001 PHE F 170 TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00324 (13090) covalent geometry : angle 0.46828 (17600) hydrogen bonds : bond 0.04370 ( 603) hydrogen bonds : angle 4.47571 ( 1785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8460 (mt) REVERT: I 255 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6706 (mm-30) REVERT: B 255 GLU cc_start: 0.6070 (mm-30) cc_final: 0.5696 (mm-30) REVERT: E 125 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7044 (mtmm) REVERT: E 230 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 178 MET cc_start: 0.8797 (mmm) cc_final: 0.7588 (mmm) REVERT: F 185 ASP cc_start: 0.8517 (t0) cc_final: 0.8284 (t0) REVERT: H 135 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8435 (mt) REVERT: H 174 TYR cc_start: 0.7667 (m-80) cc_final: 0.7014 (m-80) REVERT: H 255 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6432 (mm-30) REVERT: J 255 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6232 (mm-30) REVERT: J 262 ASN cc_start: 0.8598 (m110) cc_final: 0.8247 (m110) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.2415 time to fit residues: 61.3447 Evaluate side-chains 163 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 264 LYS Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 174 TYR Chi-restraints excluded: chain J residue 227 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.135103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122972 restraints weight = 42478.686| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.42 r_work: 0.3501 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13090 Z= 0.098 Angle : 0.434 4.545 17600 Z= 0.241 Chirality : 0.039 0.136 1890 Planarity : 0.003 0.031 2200 Dihedral : 3.929 50.495 1672 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.91 % Allowed : 19.58 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1540 helix: 2.80 (0.18), residues: 750 sheet: -3.99 (0.32), residues: 150 loop : -0.90 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 243 TYR 0.013 0.001 TYR G 177 PHE 0.007 0.001 PHE E 131 TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00223 (13090) covalent geometry : angle 0.43442 (17600) hydrogen bonds : bond 0.03656 ( 603) hydrogen bonds : angle 4.25709 ( 1785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.51 seconds wall clock time: 87 minutes 46.62 seconds (5266.62 seconds total)