Starting phenix.real_space_refine on Fri Sep 11 03:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.map" model { file = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mi7_9125/09_2026/6mi7_9125.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 C 4713 2.51 5 N 1240 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7285 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "G" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain breaks: 3 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.24 Number of scatterers: 7285 At special positions: 0 Unit cell: (81.18, 102.09, 109.47, 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 43 16.00 P 1 15.00 O 1288 8.00 N 1240 7.00 C 4713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 545.3 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 51.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.553A pdb=" N LEU F 7 " --> pdb=" O ILE F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 24 removed outlier: 3.709A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.569A pdb=" N PHE F 69 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 removed outlier: 3.670A pdb=" N MET F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 119 removed outlier: 3.551A pdb=" N VAL F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.546A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR F 275 " --> pdb=" O THR F 271 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET F 278 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 Processing helix chain 'F' and resid 299 through 319 removed outlier: 3.896A pdb=" N LEU F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR F 314 " --> pdb=" O PHE F 310 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 345 removed outlier: 3.703A pdb=" N TYR F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 33 removed outlier: 3.533A pdb=" N ILE G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 12 " --> pdb=" O ASP G 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU G 23 " --> pdb=" O ILE G 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 59 Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.114A pdb=" N ASP G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 59 through 64' Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 98 through 109 removed outlier: 3.648A pdb=" N VAL G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 131 removed outlier: 3.723A pdb=" N MET G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.580A pdb=" N ARG G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.578A pdb=" N LEU G 273 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE G 280 " --> pdb=" O TRP G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 293 removed outlier: 4.038A pdb=" N ALA G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 290 " --> pdb=" O ALA G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 318 removed outlier: 4.420A pdb=" N GLY G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 318 " --> pdb=" O SER G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 removed outlier: 3.521A pdb=" N GLN G 324 " --> pdb=" O TYR G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 333 removed outlier: 3.651A pdb=" N THR G 330 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 356 removed outlier: 3.851A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER G 352 " --> pdb=" O PHE G 348 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.635A pdb=" N MET A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.712A pdb=" N GLN A 104 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.578A pdb=" N ASP A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 4.068A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.916A pdb=" N ILE A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.721A pdb=" N THR A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.502A pdb=" N THR B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.996A pdb=" N ALA B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.587A pdb=" N MET B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.171A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.773A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 removed outlier: 3.572A pdb=" N ARG B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.589A pdb=" N LEU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'C' and resid 4 through 21 removed outlier: 3.876A pdb=" N ILE C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 11 " --> pdb=" O TRP C 7 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 27 removed outlier: 5.269A pdb=" N LEU A 9 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 23 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS A 7 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 25 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR A 5 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN A 27 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR A 3 " --> pdb=" O ASN A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 7.297A pdb=" N ILE A 159 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.526A pdb=" N LYS B 11 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 61 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 9 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.809A pdb=" N LEU B 191 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY B 81 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 162 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 83 " --> pdb=" O ASP B 162 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 660 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: 0.98 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2100 1.33 - 1.45: 1009 1.45 - 1.57: 4213 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 7406 Sorted by residual: bond pdb=" C11 PGT F 401 " pdb=" O3 PGT F 401 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C31 PGT F 401 " pdb=" O2 PGT F 401 " ideal model delta sigma weight residual 1.331 1.450 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C LEU F 300 " pdb=" N PRO F 301 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.65e+00 bond pdb=" O3P PGT F 401 " pdb=" P PGT F 401 " ideal model delta sigma weight residual 1.640 1.603 0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" O4P PGT F 401 " pdb=" P PGT F 401 " ideal model delta sigma weight residual 1.641 1.606 0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 7401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9673 2.72 - 5.45: 263 5.45 - 8.17: 63 8.17 - 10.89: 22 10.89 - 13.61: 2 Bond angle restraints: 10023 Sorted by residual: angle pdb=" N VAL B 230 " pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 113.71 106.45 7.26 9.50e-01 1.11e+00 5.84e+01 angle pdb=" N ILE A 171 " pdb=" CA ILE A 171 " pdb=" C ILE A 171 " ideal model delta sigma weight residual 111.91 105.59 6.32 8.90e-01 1.26e+00 5.04e+01 angle pdb=" N ILE B 216 " pdb=" CA ILE B 216 " pdb=" C ILE B 216 " ideal model delta sigma weight residual 112.43 107.05 5.38 9.20e-01 1.18e+00 3.42e+01 angle pdb=" N VAL A 230 " pdb=" CA VAL A 230 " pdb=" C VAL A 230 " ideal model delta sigma weight residual 112.80 106.98 5.82 1.15e+00 7.56e-01 2.56e+01 angle pdb=" C LEU F 266 " pdb=" N ASN F 267 " pdb=" CA ASN F 267 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 ... (remaining 10018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 4076 15.55 - 31.10: 292 31.10 - 46.64: 92 46.64 - 62.19: 12 62.19 - 77.74: 5 Dihedral angle restraints: 4477 sinusoidal: 1802 harmonic: 2675 Sorted by residual: dihedral pdb=" CA ASN F 290 " pdb=" C ASN F 290 " pdb=" N PRO F 291 " pdb=" CA PRO F 291 " ideal model delta harmonic sigma weight residual -180.00 -147.24 -32.76 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA PHE B 90 " pdb=" C PHE B 90 " pdb=" N ARG B 91 " pdb=" CA ARG B 91 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE G 280 " pdb=" C PHE G 280 " pdb=" N GLN G 281 " pdb=" CA GLN G 281 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 4474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1074 0.090 - 0.179: 116 0.179 - 0.269: 11 0.269 - 0.358: 3 0.358 - 0.448: 1 Chirality restraints: 1205 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CB ILE A 62 " pdb=" CA ILE A 62 " pdb=" CG1 ILE A 62 " pdb=" CG2 ILE A 62 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB VAL G 258 " pdb=" CA VAL G 258 " pdb=" CG1 VAL G 258 " pdb=" CG2 VAL G 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 1202 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 284 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO F 285 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 285 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 285 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 327 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO G 328 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 335 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO G 336 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 336 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 336 " 0.036 5.00e-02 4.00e+02 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 62 2.62 - 3.19: 6058 3.19 - 3.76: 10728 3.76 - 4.33: 14294 4.33 - 4.90: 22444 Nonbonded interactions: 53586 Sorted by model distance: nonbonded pdb=" O1P PGT F 401 " pdb=" O5 PGT F 401 " model vdw 2.053 3.040 nonbonded pdb=" OG1 THR A 220 " pdb=" OE1 GLU A 223 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OE1 GLU A 115 " model vdw 2.342 3.040 nonbonded pdb=" O SER A 88 " pdb=" NH2 ARG A 150 " model vdw 2.352 3.120 nonbonded pdb=" OE2 GLU F 82 " pdb=" NH1 ARG B 91 " model vdw 2.353 3.120 ... (remaining 53581 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' } 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 group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 7406 Z= 0.261 Angle : 1.187 13.614 10023 Z= 0.592 Chirality : 0.062 0.448 1205 Planarity : 0.008 0.067 1246 Dihedral : 12.423 77.741 2745 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.38 % Allowed : 9.29 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -5.97 (0.19), residues: 911 helix: -4.39 (0.11), residues: 436 sheet: -3.55 (0.43), residues: 78 loop : -3.37 (0.25), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.039 0.002 TYR F 80 PHE 0.039 0.003 PHE G 67 TRP 0.014 0.002 TRP G 276 HIS 0.009 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 ( 7406) covalent geometry : angle 1.18682 / 0.59 (10023) hydrogen bonds : bond 0.30556 / 19.84 ( 229) hydrogen bonds : angle 10.41381 / 7.08 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 373 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 6 TYR cc_start: 0.9254 (t80) cc_final: 0.8530 (t80) REVERT: F 59 MET cc_start: 0.5990 (tpp) cc_final: 0.5543 (ptt) REVERT: F 78 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7677 (ttmt) REVERT: F 281 LEU cc_start: 0.9068 (tt) cc_final: 0.8755 (tt) REVERT: F 297 LEU cc_start: 0.9472 (tp) cc_final: 0.9253 (tp) REVERT: F 314 THR cc_start: 0.9276 (p) cc_final: 0.8947 (m) REVERT: G 90 VAL cc_start: 0.9491 (m) cc_final: 0.9180 (t) REVERT: G 100 MET cc_start: 0.7296 (tpp) cc_final: 0.6866 (tpp) REVERT: G 108 LYS cc_start: 0.7410 (tmtt) cc_final: 0.6753 (tttt) REVERT: G 254 LEU cc_start: 0.9044 (tp) cc_final: 0.8818 (mm) REVERT: G 278 LYS cc_start: 0.9115 (ttmp) cc_final: 0.8825 (mtpt) REVERT: G 351 ILE cc_start: 0.9169 (mt) cc_final: 0.8928 (mt) REVERT: G 356 LEU cc_start: 0.7557 (pp) cc_final: 0.7352 (pp) REVERT: A 8 ASN cc_start: 0.8481 (m110) cc_final: 0.8089 (m110) REVERT: A 11 LYS cc_start: 0.8850 (tptp) cc_final: 0.8180 (tptm) REVERT: A 21 ASP cc_start: 0.7834 (t0) cc_final: 0.7451 (p0) REVERT: A 98 ASN cc_start: 0.8835 (t0) cc_final: 0.8404 (t0) REVERT: A 104 GLN cc_start: 0.8545 (mt0) cc_final: 0.8334 (mm110) REVERT: A 108 ASP cc_start: 0.9002 (p0) cc_final: 0.8693 (p0) REVERT: A 116 ASP cc_start: 0.7986 (m-30) cc_final: 0.7679 (t0) REVERT: A 123 GLU cc_start: 0.8180 (pt0) cc_final: 0.6570 (tm-30) REVERT: A 128 GLU cc_start: 0.7529 (pm20) cc_final: 0.6904 (pm20) REVERT: A 137 SER cc_start: 0.8660 (p) cc_final: 0.8417 (p) REVERT: A 155 ASN cc_start: 0.7942 (t0) cc_final: 0.7655 (t0) REVERT: A 162 ASP cc_start: 0.9048 (t0) cc_final: 0.8799 (t0) REVERT: A 185 ASP cc_start: 0.8635 (t70) cc_final: 0.8207 (t0) REVERT: A 220 THR cc_start: 0.7163 (p) cc_final: 0.6933 (m) REVERT: B 19 VAL cc_start: 0.9139 (t) cc_final: 0.8878 (t) REVERT: B 44 THR cc_start: 0.8961 (m) cc_final: 0.8626 (m) REVERT: B 82 TYR cc_start: 0.9066 (t80) cc_final: 0.8634 (t80) REVERT: B 95 VAL cc_start: 0.9148 (t) cc_final: 0.8935 (p) REVERT: B 100 MET cc_start: 0.8361 (mmm) cc_final: 0.7932 (mmm) REVERT: B 113 GLN cc_start: 0.7647 (pm20) cc_final: 0.7365 (pm20) REVERT: B 121 LEU cc_start: 0.9155 (tp) cc_final: 0.8823 (tt) REVERT: B 126 HIS cc_start: 0.8156 (m-70) cc_final: 0.7482 (m170) REVERT: B 145 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8558 (mtm180) REVERT: B 169 ASP cc_start: 0.8616 (p0) cc_final: 0.8409 (p0) REVERT: C 6 ARG cc_start: 0.7707 (mtp180) cc_final: 0.5994 (ptt180) outliers start: 3 outliers final: 0 residues processed: 374 average time/residue: 0.0904 time to fit residues: 44.6634 Evaluate side-chains 264 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 85 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115465 restraints weight = 12323.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118018 restraints weight = 8141.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119621 restraints weight = 6111.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120936 restraints weight = 5068.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121638 restraints weight = 4444.414| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7406 Z= 0.156 Angle : 0.753 11.165 10023 Z= 0.380 Chirality : 0.045 0.224 1205 Planarity : 0.006 0.048 1246 Dihedral : 8.011 59.411 1035 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.25 % Allowed : 4.71 % Favored : 95.04 % 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: -4.57 (0.23), residues: 911 helix: -2.95 (0.19), residues: 457 sheet: -3.08 (0.48), residues: 68 loop : -2.96 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.022 0.001 TYR F 80 PHE 0.041 0.002 PHE G 67 TRP 0.014 0.001 TRP F 330 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7406) covalent geometry : angle 0.75282 / 0.38 (10023) hydrogen bonds : bond 0.05305 / 3.46 ( 229) hydrogen bonds : angle 6.14487 / 4.03 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 5 ARG cc_start: 0.8392 (ttt-90) cc_final: 0.8014 (ttp80) REVERT: F 59 MET cc_start: 0.5929 (tpp) cc_final: 0.5339 (ptt) REVERT: F 105 LEU cc_start: 0.9237 (pp) cc_final: 0.9036 (pp) REVERT: F 279 MET cc_start: 0.8800 (mmp) cc_final: 0.7748 (mmp) REVERT: G 20 MET cc_start: 0.6854 (tmm) cc_final: 0.6379 (tmm) REVERT: G 90 VAL cc_start: 0.9526 (m) cc_final: 0.9136 (t) REVERT: G 100 MET cc_start: 0.7287 (tpp) cc_final: 0.6973 (tpp) REVERT: G 108 LYS cc_start: 0.7311 (tmtt) cc_final: 0.6910 (tttt) REVERT: G 113 LEU cc_start: 0.9301 (tp) cc_final: 0.9047 (tt) REVERT: G 356 LEU cc_start: 0.7850 (pp) cc_final: 0.7551 (pp) REVERT: G 357 MET cc_start: 0.7639 (mmt) cc_final: 0.7383 (mmt) REVERT: A 9 LEU cc_start: 0.9284 (mt) cc_final: 0.8993 (mp) REVERT: A 59 ASN cc_start: 0.8739 (m110) cc_final: 0.8465 (m110) REVERT: A 98 ASN cc_start: 0.8768 (t0) cc_final: 0.8361 (t0) REVERT: A 116 ASP cc_start: 0.7929 (m-30) cc_final: 0.7630 (t0) REVERT: A 123 GLU cc_start: 0.8174 (pt0) cc_final: 0.6931 (tm-30) REVERT: A 128 GLU cc_start: 0.7519 (pm20) cc_final: 0.6819 (pm20) REVERT: A 155 ASN cc_start: 0.8072 (t0) cc_final: 0.7779 (t0) REVERT: A 185 ASP cc_start: 0.8509 (t70) cc_final: 0.8221 (t0) REVERT: A 220 THR cc_start: 0.7749 (p) cc_final: 0.6600 (p) REVERT: B 67 ILE cc_start: 0.9216 (pt) cc_final: 0.8999 (pt) REVERT: B 82 TYR cc_start: 0.8859 (t80) cc_final: 0.8419 (t80) REVERT: B 121 LEU cc_start: 0.8878 (tp) cc_final: 0.8671 (tt) REVERT: B 126 HIS cc_start: 0.8190 (m-70) cc_final: 0.7104 (m170) REVERT: B 145 ARG cc_start: 0.9114 (mtm-85) cc_final: 0.8360 (mtp85) REVERT: B 169 ASP cc_start: 0.8756 (p0) cc_final: 0.8475 (p0) REVERT: B 212 GLN cc_start: 0.9005 (mp10) cc_final: 0.8134 (mp10) REVERT: C 6 ARG cc_start: 0.7630 (mtp180) cc_final: 0.6218 (ptt180) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.0790 time to fit residues: 35.3541 Evaluate side-chains 259 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112916 restraints weight = 12302.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115292 restraints weight = 8325.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116730 restraints weight = 6368.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117972 restraints weight = 5360.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118644 restraints weight = 4742.611| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7406 Z= 0.139 Angle : 0.712 11.045 10023 Z= 0.356 Chirality : 0.044 0.235 1205 Planarity : 0.005 0.048 1246 Dihedral : 7.394 59.181 1035 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.91 % 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: -3.73 (0.25), residues: 911 helix: -2.20 (0.22), residues: 458 sheet: -2.70 (0.50), residues: 68 loop : -2.64 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 6 TYR 0.029 0.001 TYR F 80 PHE 0.030 0.002 PHE G 67 TRP 0.011 0.001 TRP F 330 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7406) covalent geometry : angle 0.71195 / 0.36 (10023) hydrogen bonds : bond 0.03985 / 2.61 ( 229) hydrogen bonds : angle 5.54471 / 3.65 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.6061 (tpp) cc_final: 0.5402 (ptt) REVERT: G 20 MET cc_start: 0.6848 (tmm) cc_final: 0.6535 (tmm) REVERT: G 78 LEU cc_start: 0.9062 (tp) cc_final: 0.8827 (tt) REVERT: G 90 VAL cc_start: 0.9541 (m) cc_final: 0.9177 (t) REVERT: G 100 MET cc_start: 0.7493 (tpp) cc_final: 0.6999 (tpp) REVERT: G 108 LYS cc_start: 0.7434 (tmtt) cc_final: 0.6828 (tttt) REVERT: G 120 ILE cc_start: 0.8948 (pt) cc_final: 0.8610 (mm) REVERT: G 356 LEU cc_start: 0.7804 (pp) cc_final: 0.7572 (pp) REVERT: G 357 MET cc_start: 0.7722 (mmt) cc_final: 0.7419 (mmt) REVERT: A 9 LEU cc_start: 0.9359 (mt) cc_final: 0.9099 (mt) REVERT: A 48 MET cc_start: 0.8075 (ttm) cc_final: 0.7621 (ttp) REVERT: A 98 ASN cc_start: 0.8727 (t0) cc_final: 0.8364 (t0) REVERT: A 107 ASP cc_start: 0.7779 (p0) cc_final: 0.7119 (m-30) REVERT: A 116 ASP cc_start: 0.7992 (m-30) cc_final: 0.7647 (t0) REVERT: A 123 GLU cc_start: 0.8193 (pt0) cc_final: 0.7391 (tm-30) REVERT: A 128 GLU cc_start: 0.7657 (pm20) cc_final: 0.6594 (pm20) REVERT: A 155 ASN cc_start: 0.8162 (t0) cc_final: 0.7872 (t0) REVERT: A 220 THR cc_start: 0.7615 (p) cc_final: 0.6216 (t) REVERT: B 8 ASN cc_start: 0.7842 (m110) cc_final: 0.6764 (m110) REVERT: B 67 ILE cc_start: 0.9134 (pt) cc_final: 0.8862 (pt) REVERT: B 68 SER cc_start: 0.8740 (m) cc_final: 0.8286 (p) REVERT: B 82 TYR cc_start: 0.8850 (t80) cc_final: 0.8368 (t80) REVERT: B 100 MET cc_start: 0.7671 (mmm) cc_final: 0.7359 (mmm) REVERT: B 122 MET cc_start: 0.8683 (mtt) cc_final: 0.8389 (mtm) REVERT: B 126 HIS cc_start: 0.8185 (m-70) cc_final: 0.7456 (m170) REVERT: B 145 ARG cc_start: 0.9148 (mtm-85) cc_final: 0.8498 (mtm180) REVERT: B 169 ASP cc_start: 0.8757 (p0) cc_final: 0.8542 (p0) REVERT: C 6 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6053 (ptt180) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.0804 time to fit residues: 34.7859 Evaluate side-chains 253 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** B 73 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.137520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112095 restraints weight = 12527.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114725 restraints weight = 8250.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116509 restraints weight = 6151.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117411 restraints weight = 5057.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118268 restraints weight = 4510.306| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7406 Z= 0.128 Angle : 0.702 10.607 10023 Z= 0.346 Chirality : 0.045 0.225 1205 Planarity : 0.005 0.047 1246 Dihedral : 7.111 55.557 1035 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.25 % Allowed : 3.44 % Favored : 96.31 % 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: -3.20 (0.26), residues: 911 helix: -1.74 (0.23), residues: 455 sheet: -2.24 (0.54), residues: 68 loop : -2.45 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 133 TYR 0.024 0.001 TYR F 80 PHE 0.020 0.001 PHE A 165 TRP 0.009 0.001 TRP F 330 HIS 0.002 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7406) covalent geometry : angle 0.70197 / 0.35 (10023) hydrogen bonds : bond 0.03658 / 2.40 ( 229) hydrogen bonds : angle 5.27277 / 3.46 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5846 (tpp) cc_final: 0.5310 (ptt) REVERT: F 279 MET cc_start: 0.8676 (mmm) cc_final: 0.8462 (mmp) REVERT: G 20 MET cc_start: 0.7094 (tmm) cc_final: 0.6725 (tmm) REVERT: G 90 VAL cc_start: 0.9434 (m) cc_final: 0.9167 (t) REVERT: G 100 MET cc_start: 0.7431 (tpp) cc_final: 0.7120 (tpp) REVERT: G 108 LYS cc_start: 0.7624 (tmtt) cc_final: 0.6976 (tttt) REVERT: G 118 MET cc_start: 0.7995 (mmm) cc_final: 0.7776 (mmt) REVERT: G 120 ILE cc_start: 0.8903 (pt) cc_final: 0.8544 (mm) REVERT: G 357 MET cc_start: 0.7774 (mmt) cc_final: 0.7489 (mmt) REVERT: A 42 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8138 (mtmm) REVERT: A 98 ASN cc_start: 0.8639 (t0) cc_final: 0.8318 (t0) REVERT: A 107 ASP cc_start: 0.7685 (p0) cc_final: 0.7017 (m-30) REVERT: A 155 ASN cc_start: 0.8079 (t0) cc_final: 0.7866 (t0) REVERT: A 220 THR cc_start: 0.7244 (p) cc_final: 0.5457 (t) REVERT: B 67 ILE cc_start: 0.9138 (pt) cc_final: 0.8929 (pt) REVERT: B 68 SER cc_start: 0.8799 (m) cc_final: 0.8396 (p) REVERT: B 82 TYR cc_start: 0.8745 (t80) cc_final: 0.8316 (t80) REVERT: B 109 LEU cc_start: 0.7008 (mm) cc_final: 0.6739 (mm) REVERT: B 122 MET cc_start: 0.8251 (mtt) cc_final: 0.7975 (mtm) REVERT: B 126 HIS cc_start: 0.7903 (m-70) cc_final: 0.7257 (m170) REVERT: B 145 ARG cc_start: 0.9072 (mtm-85) cc_final: 0.8453 (mtm180) REVERT: B 169 ASP cc_start: 0.8583 (p0) cc_final: 0.8361 (p0) REVERT: C 6 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6126 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 307 average time/residue: 0.0804 time to fit residues: 33.8471 Evaluate side-chains 245 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN A 8 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115976 restraints weight = 12346.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118491 restraints weight = 8199.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119975 restraints weight = 6186.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121232 restraints weight = 5165.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122164 restraints weight = 4548.056| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7406 Z= 0.136 Angle : 0.697 12.106 10023 Z= 0.341 Chirality : 0.045 0.236 1205 Planarity : 0.005 0.046 1246 Dihedral : 6.967 55.741 1035 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -2.89 (0.27), residues: 911 helix: -1.43 (0.24), residues: 461 sheet: -2.00 (0.55), residues: 68 loop : -2.40 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 133 TYR 0.033 0.001 TYR F 80 PHE 0.028 0.002 PHE G 67 TRP 0.009 0.001 TRP F 330 HIS 0.003 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7406) covalent geometry : angle 0.69659 / 0.34 (10023) hydrogen bonds : bond 0.03536 / 2.32 ( 229) hydrogen bonds : angle 5.06766 / 3.35 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: F 59 MET cc_start: 0.5853 (tpp) cc_final: 0.5263 (ptt) REVERT: F 78 LYS cc_start: 0.8297 (tttt) cc_final: 0.7502 (tptt) REVERT: F 86 THR cc_start: 0.9223 (m) cc_final: 0.9012 (m) REVERT: F 278 MET cc_start: 0.8954 (ttp) cc_final: 0.8511 (ttt) REVERT: G 20 MET cc_start: 0.7075 (tmm) cc_final: 0.6691 (tmm) REVERT: G 28 SER cc_start: 0.8853 (m) cc_final: 0.8368 (t) REVERT: G 62 LYS cc_start: 0.8875 (tptt) cc_final: 0.8640 (tptm) REVERT: G 90 VAL cc_start: 0.9571 (m) cc_final: 0.9294 (t) REVERT: G 100 MET cc_start: 0.7895 (tpp) cc_final: 0.7570 (tpp) REVERT: G 108 LYS cc_start: 0.7551 (tmtt) cc_final: 0.6894 (tttt) REVERT: G 120 ILE cc_start: 0.8852 (pt) cc_final: 0.8587 (mm) REVERT: G 288 MET cc_start: 0.8709 (mmt) cc_final: 0.8486 (mmp) REVERT: G 354 TRP cc_start: 0.8405 (t60) cc_final: 0.8162 (t60) REVERT: G 356 LEU cc_start: 0.7925 (pp) cc_final: 0.7500 (pp) REVERT: A 9 LEU cc_start: 0.9241 (mt) cc_final: 0.8520 (mm) REVERT: A 42 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8232 (mtmm) REVERT: A 48 MET cc_start: 0.8319 (ttm) cc_final: 0.7817 (ttp) REVERT: A 107 ASP cc_start: 0.7931 (p0) cc_final: 0.7196 (m-30) REVERT: A 155 ASN cc_start: 0.8285 (t0) cc_final: 0.8049 (t0) REVERT: A 162 ASP cc_start: 0.9005 (t70) cc_final: 0.8690 (t0) REVERT: A 220 THR cc_start: 0.7344 (p) cc_final: 0.5838 (t) REVERT: B 8 ASN cc_start: 0.7858 (m110) cc_final: 0.6701 (m-40) REVERT: B 67 ILE cc_start: 0.9164 (pt) cc_final: 0.8945 (pt) REVERT: B 68 SER cc_start: 0.8803 (m) cc_final: 0.8477 (p) REVERT: B 82 TYR cc_start: 0.8805 (t80) cc_final: 0.8407 (t80) REVERT: B 122 MET cc_start: 0.8566 (mtt) cc_final: 0.8325 (mtm) REVERT: B 126 HIS cc_start: 0.8240 (m-70) cc_final: 0.7741 (m170) REVERT: B 145 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8477 (mtm180) REVERT: B 169 ASP cc_start: 0.8734 (p0) cc_final: 0.8485 (p0) REVERT: B 186 SER cc_start: 0.9148 (m) cc_final: 0.8730 (p) REVERT: C 6 ARG cc_start: 0.7207 (mtp180) cc_final: 0.5971 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.0797 time to fit residues: 31.8186 Evaluate side-chains 251 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 0.0980 chunk 3 optimal weight: 0.0040 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 85 GLN ** B 73 HIS ** 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 = 0.3575 r_free = 0.3575 target = 0.141103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116697 restraints weight = 12424.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119208 restraints weight = 8323.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120877 restraints weight = 6318.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122060 restraints weight = 5251.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122678 restraints weight = 4647.114| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7406 Z= 0.110 Angle : 0.680 11.899 10023 Z= 0.329 Chirality : 0.043 0.239 1205 Planarity : 0.004 0.047 1246 Dihedral : 6.628 57.919 1035 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % 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: -2.52 (0.28), residues: 911 helix: -1.14 (0.25), residues: 462 sheet: -1.91 (0.65), residues: 56 loop : -2.20 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.018 0.001 TYR A 96 PHE 0.026 0.001 PHE G 67 TRP 0.007 0.001 TRP F 330 HIS 0.002 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7406) covalent geometry : angle 0.67979 / 0.33 (10023) hydrogen bonds : bond 0.03119 / 2.07 ( 229) hydrogen bonds : angle 4.91663 / 3.24 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5883 (tpp) cc_final: 0.5377 (ptt) REVERT: F 72 LEU cc_start: 0.9425 (tp) cc_final: 0.9178 (tp) REVERT: F 78 LYS cc_start: 0.8234 (tttt) cc_final: 0.7524 (tptt) REVERT: G 20 MET cc_start: 0.7108 (tmm) cc_final: 0.6872 (tmm) REVERT: G 28 SER cc_start: 0.8785 (m) cc_final: 0.8200 (t) REVERT: G 100 MET cc_start: 0.7467 (tpp) cc_final: 0.6889 (tpp) REVERT: G 108 LYS cc_start: 0.7620 (tmtt) cc_final: 0.6968 (tttt) REVERT: G 120 ILE cc_start: 0.8725 (pt) cc_final: 0.8424 (mm) REVERT: G 356 LEU cc_start: 0.7499 (pp) cc_final: 0.7248 (pp) REVERT: A 9 LEU cc_start: 0.9257 (mt) cc_final: 0.8697 (mm) REVERT: A 42 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8214 (mtmm) REVERT: A 48 MET cc_start: 0.8098 (ttm) cc_final: 0.7660 (ttp) REVERT: A 107 ASP cc_start: 0.7709 (p0) cc_final: 0.7107 (m-30) REVERT: A 108 ASP cc_start: 0.8724 (p0) cc_final: 0.8371 (p0) REVERT: A 123 GLU cc_start: 0.8108 (pt0) cc_final: 0.7207 (tm-30) REVERT: A 162 ASP cc_start: 0.9216 (t70) cc_final: 0.8678 (t0) REVERT: B 64 ASP cc_start: 0.7867 (m-30) cc_final: 0.7631 (m-30) REVERT: B 82 TYR cc_start: 0.8644 (t80) cc_final: 0.8242 (t80) REVERT: B 126 HIS cc_start: 0.7997 (m-70) cc_final: 0.7451 (m170) REVERT: B 145 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8466 (mtm180) REVERT: B 162 ASP cc_start: 0.8512 (t0) cc_final: 0.8078 (t0) REVERT: B 186 SER cc_start: 0.8990 (m) cc_final: 0.8710 (p) REVERT: C 6 ARG cc_start: 0.7267 (mtp180) cc_final: 0.6368 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.0746 time to fit residues: 31.3679 Evaluate side-chains 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 82 optimal weight: 0.0050 chunk 28 optimal weight: 0.0970 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 73 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.148249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124469 restraints weight = 12238.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127135 restraints weight = 7927.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129044 restraints weight = 5874.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130267 restraints weight = 4791.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131016 restraints weight = 4182.394| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7406 Z= 0.113 Angle : 0.705 12.131 10023 Z= 0.334 Chirality : 0.044 0.225 1205 Planarity : 0.005 0.046 1246 Dihedral : 6.331 59.955 1035 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -2.37 (0.27), residues: 911 helix: -1.05 (0.24), residues: 463 sheet: -1.66 (0.64), residues: 58 loop : -2.12 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 133 TYR 0.018 0.001 TYR B 96 PHE 0.058 0.002 PHE G 67 TRP 0.007 0.001 TRP F 268 HIS 0.003 0.000 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 7406) covalent geometry : angle 0.70498 / 0.33 (10023) hydrogen bonds : bond 0.02868 / 1.85 ( 229) hydrogen bonds : angle 4.82181 / 3.22 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5801 (tpp) cc_final: 0.5215 (ptt) REVERT: F 72 LEU cc_start: 0.9347 (tp) cc_final: 0.9092 (tp) REVERT: G 20 MET cc_start: 0.7029 (tmm) cc_final: 0.6776 (tmm) REVERT: G 28 SER cc_start: 0.8689 (m) cc_final: 0.8168 (t) REVERT: G 62 LYS cc_start: 0.8941 (tptt) cc_final: 0.8427 (tppt) REVERT: G 100 MET cc_start: 0.7493 (tpp) cc_final: 0.6945 (tpp) REVERT: G 108 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7222 (tttt) REVERT: G 120 ILE cc_start: 0.8708 (pt) cc_final: 0.8255 (mm) REVERT: A 9 LEU cc_start: 0.9126 (mt) cc_final: 0.8718 (mm) REVERT: A 48 MET cc_start: 0.8294 (ttm) cc_final: 0.8067 (ttm) REVERT: A 107 ASP cc_start: 0.7716 (p0) cc_final: 0.7013 (m-30) REVERT: A 108 ASP cc_start: 0.8735 (p0) cc_final: 0.8442 (p0) REVERT: A 123 GLU cc_start: 0.8142 (pt0) cc_final: 0.7235 (tm-30) REVERT: A 162 ASP cc_start: 0.9188 (t70) cc_final: 0.8659 (t0) REVERT: A 194 ASP cc_start: 0.7533 (t0) cc_final: 0.7302 (t0) REVERT: A 220 THR cc_start: 0.6541 (t) cc_final: 0.4695 (m) REVERT: B 8 ASN cc_start: 0.7913 (m110) cc_final: 0.7090 (m-40) REVERT: B 82 TYR cc_start: 0.8740 (t80) cc_final: 0.8230 (t80) REVERT: B 126 HIS cc_start: 0.7976 (m-70) cc_final: 0.7443 (m170) REVERT: B 145 ARG cc_start: 0.9060 (mtm-85) cc_final: 0.8532 (mtm180) REVERT: B 186 SER cc_start: 0.8951 (m) cc_final: 0.8653 (p) REVERT: C 6 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6292 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.0749 time to fit residues: 32.0962 Evaluate side-chains 247 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 128 GLN B 27 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.111554 restraints weight = 12708.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114232 restraints weight = 8276.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115867 restraints weight = 6199.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117183 restraints weight = 5133.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117769 restraints weight = 4505.212| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7406 Z= 0.167 Angle : 0.786 13.253 10023 Z= 0.381 Chirality : 0.047 0.228 1205 Planarity : 0.005 0.046 1246 Dihedral : 6.572 59.283 1035 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -2.35 (0.28), residues: 911 helix: -1.04 (0.24), residues: 467 sheet: -1.98 (0.59), residues: 66 loop : -2.02 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 17 TYR 0.044 0.002 TYR F 80 PHE 0.054 0.002 PHE G 67 TRP 0.009 0.001 TRP F 330 HIS 0.006 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7406) covalent geometry : angle 0.78589 / 0.38 (10023) hydrogen bonds : bond 0.03428 / 2.25 ( 229) hydrogen bonds : angle 4.89943 / 3.26 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5881 (tpp) cc_final: 0.5342 (ptt) REVERT: F 282 MET cc_start: 0.8626 (tmm) cc_final: 0.8326 (tmm) REVERT: G 62 LYS cc_start: 0.9037 (tptt) cc_final: 0.8499 (tppt) REVERT: G 100 MET cc_start: 0.7543 (tpp) cc_final: 0.7067 (tpp) REVERT: G 108 LYS cc_start: 0.7712 (tmtt) cc_final: 0.7178 (tttt) REVERT: G 111 ILE cc_start: 0.8913 (pt) cc_final: 0.8658 (pt) REVERT: G 120 ILE cc_start: 0.8818 (pt) cc_final: 0.8559 (mm) REVERT: G 356 LEU cc_start: 0.7831 (pp) cc_final: 0.7519 (pp) REVERT: G 357 MET cc_start: 0.7843 (mmt) cc_final: 0.7623 (mmt) REVERT: A 9 LEU cc_start: 0.9255 (mt) cc_final: 0.8683 (mm) REVERT: A 42 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8350 (mtmm) REVERT: A 48 MET cc_start: 0.8288 (ttm) cc_final: 0.7696 (ttm) REVERT: A 107 ASP cc_start: 0.7786 (p0) cc_final: 0.7207 (m-30) REVERT: A 108 ASP cc_start: 0.8767 (p0) cc_final: 0.8444 (p0) REVERT: A 123 GLU cc_start: 0.8275 (pt0) cc_final: 0.7402 (tm-30) REVERT: A 162 ASP cc_start: 0.9215 (t70) cc_final: 0.8682 (t0) REVERT: B 82 TYR cc_start: 0.8826 (t80) cc_final: 0.8288 (t80) REVERT: B 126 HIS cc_start: 0.8008 (m-70) cc_final: 0.7476 (m170) REVERT: B 145 ARG cc_start: 0.9166 (mtm-85) cc_final: 0.8677 (mtm180) REVERT: B 186 SER cc_start: 0.9166 (m) cc_final: 0.8846 (p) REVERT: C 6 ARG cc_start: 0.7212 (mtp180) cc_final: 0.6411 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0777 time to fit residues: 31.1818 Evaluate side-chains 239 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.141683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116437 restraints weight = 12201.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119133 restraints weight = 8015.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120956 restraints weight = 5994.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121963 restraints weight = 4942.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122878 restraints weight = 4385.533| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7406 Z= 0.125 Angle : 0.752 12.614 10023 Z= 0.360 Chirality : 0.045 0.239 1205 Planarity : 0.005 0.046 1246 Dihedral : 6.190 54.671 1035 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.28), residues: 911 helix: -0.78 (0.25), residues: 459 sheet: -1.57 (0.66), residues: 56 loop : -2.04 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 133 TYR 0.018 0.001 TYR B 96 PHE 0.032 0.002 PHE G 67 TRP 0.007 0.001 TRP F 330 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 7406) covalent geometry : angle 0.75197 / 0.36 (10023) hydrogen bonds : bond 0.03008 / 1.98 ( 229) hydrogen bonds : angle 4.77240 / 3.19 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: F 59 MET cc_start: 0.5754 (tpp) cc_final: 0.5173 (ptt) REVERT: F 282 MET cc_start: 0.8833 (tmm) cc_final: 0.8562 (tmm) REVERT: G 28 SER cc_start: 0.8795 (m) cc_final: 0.8280 (t) REVERT: G 62 LYS cc_start: 0.8949 (tptt) cc_final: 0.8393 (tppt) REVERT: G 100 MET cc_start: 0.7638 (tpp) cc_final: 0.7049 (tpp) REVERT: G 108 LYS cc_start: 0.7649 (tmtt) cc_final: 0.6959 (tttt) REVERT: G 120 ILE cc_start: 0.8785 (pt) cc_final: 0.8494 (mm) REVERT: A 9 LEU cc_start: 0.9262 (mt) cc_final: 0.8725 (mm) REVERT: A 42 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8392 (mtmm) REVERT: A 48 MET cc_start: 0.8322 (ttm) cc_final: 0.7852 (ttm) REVERT: A 107 ASP cc_start: 0.7911 (p0) cc_final: 0.7227 (m-30) REVERT: A 108 ASP cc_start: 0.8777 (p0) cc_final: 0.8474 (p0) REVERT: A 123 GLU cc_start: 0.8303 (pt0) cc_final: 0.7385 (tm-30) REVERT: A 162 ASP cc_start: 0.9216 (t70) cc_final: 0.8536 (t0) REVERT: A 194 ASP cc_start: 0.7674 (t0) cc_final: 0.7400 (t0) REVERT: B 8 ASN cc_start: 0.8018 (m110) cc_final: 0.6922 (m110) REVERT: B 82 TYR cc_start: 0.8867 (t80) cc_final: 0.8291 (t80) REVERT: B 126 HIS cc_start: 0.8098 (m-70) cc_final: 0.7614 (m170) REVERT: B 186 SER cc_start: 0.9195 (m) cc_final: 0.8808 (p) REVERT: C 6 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6238 (ptm160) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.0775 time to fit residues: 31.2662 Evaluate side-chains 247 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN A 8 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117344 restraints weight = 12340.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119985 restraints weight = 8004.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121836 restraints weight = 5975.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122926 restraints weight = 4900.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123584 restraints weight = 4335.777| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7406 Z= 0.136 Angle : 0.774 11.356 10023 Z= 0.370 Chirality : 0.046 0.221 1205 Planarity : 0.005 0.046 1246 Dihedral : 6.149 51.461 1035 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.36 % 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: -2.02 (0.28), residues: 911 helix: -0.68 (0.25), residues: 459 sheet: -1.54 (0.69), residues: 56 loop : -2.04 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 133 TYR 0.013 0.001 TYR F 6 PHE 0.031 0.002 PHE G 67 TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7406) covalent geometry : angle 0.77390 / 0.37 (10023) hydrogen bonds : bond 0.03081 / 2.03 ( 229) hydrogen bonds : angle 4.80820 / 3.21 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.5685 (tpp) cc_final: 0.5167 (ptt) REVERT: F 78 LYS cc_start: 0.8290 (tttt) cc_final: 0.7486 (tptt) REVERT: F 282 MET cc_start: 0.8912 (tmm) cc_final: 0.8477 (tmm) REVERT: F 297 LEU cc_start: 0.9334 (tp) cc_final: 0.9131 (tp) REVERT: G 28 SER cc_start: 0.8828 (m) cc_final: 0.8267 (t) REVERT: G 62 LYS cc_start: 0.9012 (tptt) cc_final: 0.8467 (tppt) REVERT: G 100 MET cc_start: 0.7718 (tpp) cc_final: 0.7105 (tpp) REVERT: G 108 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7088 (tttt) REVERT: G 118 MET cc_start: 0.8064 (mmt) cc_final: 0.7768 (mmt) REVERT: G 120 ILE cc_start: 0.8717 (pt) cc_final: 0.8398 (mm) REVERT: G 357 MET cc_start: 0.7867 (mmt) cc_final: 0.7641 (mmt) REVERT: A 7 LYS cc_start: 0.8073 (tptp) cc_final: 0.7691 (mtmt) REVERT: A 9 LEU cc_start: 0.9285 (mt) cc_final: 0.8911 (mm) REVERT: A 27 ASN cc_start: 0.8685 (p0) cc_final: 0.8347 (p0) REVERT: A 42 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8401 (mtmm) REVERT: A 48 MET cc_start: 0.8397 (ttm) cc_final: 0.7877 (ttm) REVERT: A 107 ASP cc_start: 0.7964 (p0) cc_final: 0.7288 (m-30) REVERT: A 108 ASP cc_start: 0.8693 (p0) cc_final: 0.8338 (p0) REVERT: A 123 GLU cc_start: 0.8277 (pt0) cc_final: 0.7447 (tm-30) REVERT: A 162 ASP cc_start: 0.9194 (t70) cc_final: 0.8548 (t0) REVERT: A 194 ASP cc_start: 0.7681 (t0) cc_final: 0.7399 (t0) REVERT: B 82 TYR cc_start: 0.8871 (t80) cc_final: 0.8313 (t80) REVERT: B 122 MET cc_start: 0.8692 (mtm) cc_final: 0.8367 (mpp) REVERT: B 126 HIS cc_start: 0.8107 (m-70) cc_final: 0.7153 (m170) REVERT: B 145 ARG cc_start: 0.9135 (mtm-85) cc_final: 0.8475 (mtm-85) REVERT: B 186 SER cc_start: 0.9274 (m) cc_final: 0.8790 (p) REVERT: C 6 ARG cc_start: 0.7131 (mtp180) cc_final: 0.6204 (ptm160) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.0747 time to fit residues: 29.8681 Evaluate side-chains 243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116998 restraints weight = 12476.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119649 restraints weight = 8111.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121452 restraints weight = 6023.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122464 restraints weight = 4950.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123458 restraints weight = 4375.788| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7406 Z= 0.126 Angle : 0.758 11.735 10023 Z= 0.362 Chirality : 0.045 0.227 1205 Planarity : 0.005 0.046 1246 Dihedral : 5.930 48.230 1035 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.28), residues: 911 helix: -0.56 (0.25), residues: 459 sheet: -1.48 (0.68), residues: 58 loop : -1.99 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 133 TYR 0.019 0.001 TYR B 96 PHE 0.031 0.002 PHE G 67 TRP 0.007 0.001 TRP F 330 HIS 0.003 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7406) covalent geometry : angle 0.75771 / 0.36 (10023) hydrogen bonds : bond 0.03051 / 2.04 ( 229) hydrogen bonds : angle 4.78446 / 3.18 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.59 seconds wall clock time: 24 minutes 50.76 seconds (1490.76 seconds total)