Starting phenix.real_space_refine on Fri Sep 11 16:40:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8g_10121/09_2026/6s8g_10121.cif" } resolution = 3.5 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3414 atoms to isotropic. 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 6 5.49 5 S 44 5.16 5 C 4836 2.51 5 N 1290 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 7530 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1867 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1845 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.03, per 1000 atoms: 0.27 Number of scatterers: 7530 At special positions: 0 Unit cell: (111.54, 79.092, 89.232, 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 44 16.00 P 6 15.00 O 1354 8.00 N 1290 7.00 C 4836 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: 0.54 Conformation dependent library (CDL) restraints added in 469.4 milliseconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 49.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.573A pdb=" N ARG A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.836A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.594A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.500A pdb=" N VAL A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 170 through 180 removed outlier: 4.245A pdb=" N ILE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.183A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.677A pdb=" N VAL A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.572A pdb=" N ARG B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.836A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.595A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 170 through 180 removed outlier: 4.245A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 4.182A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.676A pdb=" N VAL B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 33 removed outlier: 3.581A pdb=" N THR F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 18 " --> pdb=" O SER F 14 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.957A pdb=" N ALA F 38 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 55 removed outlier: 4.212A pdb=" N GLY F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.065A pdb=" N MET F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 82 removed outlier: 3.655A pdb=" N LEU F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 69 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET F 74 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.512A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.674A pdb=" N SER F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 282 removed outlier: 3.553A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 removed outlier: 4.196A pdb=" N ALA F 302 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 308 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 310 " --> pdb=" O TYR F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 removed outlier: 3.533A pdb=" N THR F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 334 " --> pdb=" O TRP F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 334' Processing helix chain 'F' and resid 336 through 345 removed outlier: 4.215A pdb=" N ALA F 342 " --> pdb=" O TYR F 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 15 Processing helix chain 'G' and resid 15 through 41 removed outlier: 4.152A pdb=" N MET G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.911A pdb=" N GLN G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 67 through 86 removed outlier: 3.790A pdb=" N LEU G 74 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 Processing helix chain 'G' and resid 98 through 121 removed outlier: 4.147A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.571A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.611A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 258 removed outlier: 3.958A pdb=" N VAL G 258 " --> pdb=" O HIS G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.557A pdb=" N ALA G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 287 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 316 Processing helix chain 'G' and resid 317 through 322 Processing helix chain 'G' and resid 336 through 341 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.633A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 26 removed outlier: 6.905A pdb=" N GLU A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 10 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL A 22 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.940A pdb=" N GLY A 33 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 210 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A 35 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 207 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 83 removed outlier: 3.722A pdb=" N GLY A 81 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 26 removed outlier: 6.904A pdb=" N GLU B 20 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 10 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL B 22 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.940A pdb=" N GLY B 33 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL B 210 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU B 35 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 207 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS B 218 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.722A pdb=" N GLY B 81 " --> pdb=" O PHE B 158 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 666 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: 0.92 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2392 1.34 - 1.46: 1408 1.46 - 1.58: 3775 1.58 - 1.70: 4 1.70 - 1.82: 84 Bond restraints: 7663 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP A 401 " pdb=" PB ANP A 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.677 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 1.795 1.677 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" O5' ANP B 401 " pdb=" PA ANP B 401 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 7658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 10296 5.29 - 10.58: 82 10.58 - 15.87: 9 15.87 - 21.16: 0 21.16 - 26.45: 2 Bond angle restraints: 10389 Sorted by residual: angle pdb=" PB ANP B 401 " pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 126.95 100.50 26.45 3.00e+00 1.11e-01 7.77e+01 angle pdb=" PB ANP A 401 " pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 126.95 100.56 26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" CB LYS A 14 " pdb=" CG LYS A 14 " pdb=" CD LYS A 14 " ideal model delta sigma weight residual 111.30 126.05 -14.75 2.30e+00 1.89e-01 4.11e+01 angle pdb=" CB LYS B 14 " pdb=" CG LYS B 14 " pdb=" CD LYS B 14 " ideal model delta sigma weight residual 111.30 126.04 -14.74 2.30e+00 1.89e-01 4.10e+01 angle pdb=" C ILE B 62 " pdb=" N ASP B 63 " pdb=" CA ASP B 63 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 ... (remaining 10384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 4181 23.00 - 46.00: 337 46.00 - 69.01: 51 69.01 - 92.01: 11 92.01 - 115.01: 3 Dihedral angle restraints: 4583 sinusoidal: 1841 harmonic: 2742 Sorted by residual: dihedral pdb=" CA PRO B 156 " pdb=" C PRO B 156 " pdb=" N LYS B 157 " pdb=" CA LYS B 157 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO A 156 " pdb=" C PRO A 156 " pdb=" N LYS A 157 " pdb=" CA LYS A 157 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS B 157 " pdb=" C LYS B 157 " pdb=" N PHE B 158 " pdb=" CA PHE B 158 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 4580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 863 0.056 - 0.112: 293 0.112 - 0.169: 62 0.169 - 0.225: 11 0.225 - 0.281: 4 Chirality restraints: 1233 Sorted by residual: chirality pdb=" C3' ANP A 401 " pdb=" C2' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1230 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 170 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 169 " -0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO B 170 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 64 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO F 65 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 65 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 65 " 0.039 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2282 2.82 - 3.34: 6359 3.34 - 3.86: 11586 3.86 - 4.38: 14162 4.38 - 4.90: 23901 Nonbonded interactions: 58290 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.294 3.040 nonbonded pdb=" OG SER B 139 " pdb=" OE1 GLU B 142 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 186 " pdb=" OG SER A 186 " model vdw 2.315 3.040 nonbonded pdb=" O SER B 186 " pdb=" OG SER B 186 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR G 10 " pdb=" OE1 GLU G 88 " model vdw 2.322 3.040 ... (remaining 58285 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' and ((resid 2 and (name CA or name C or name O or name CB )) or resid \ 3 through 401)) selection = (chain 'B' and (resid 2 through 239 or resid 401)) } 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.110 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.010 0.154 7663 Z= 0.427 Angle : 1.323 26.452 10389 Z= 0.673 Chirality : 0.061 0.281 1233 Planarity : 0.008 0.097 1292 Dihedral : 17.192 115.010 2815 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.74 % Favored : 85.15 % Rotamer: Outliers : 3.86 % Allowed : 12.58 % Favored : 83.56 % 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: -6.67 (0.17), residues: 943 helix: -4.89 (0.08), residues: 478 sheet: -2.08 (0.67), residues: 42 loop : -4.01 (0.24), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 198 TYR 0.016 0.002 TYR F 306 PHE 0.024 0.003 PHE G 280 TRP 0.012 0.002 TRP F 255 HIS 0.008 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.43 ( 7663) covalent geometry : angle 1.32290 / 0.67 (10389) hydrogen bonds : bond 0.29925 / 20.45 ( 233) hydrogen bonds : angle 11.19427 / 7.63 ( 666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.191 Fit side-chains REVERT: A 115 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: A 120 GLU cc_start: 0.7886 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 183 LEU cc_start: 0.9422 (mt) cc_final: 0.9066 (mp) REVERT: B 14 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7373 (ttmt) REVERT: B 69 LEU cc_start: 0.8738 (pt) cc_final: 0.8536 (pp) REVERT: B 86 GLU cc_start: 0.7871 (pm20) cc_final: 0.7647 (pm20) REVERT: B 222 THR cc_start: 0.8940 (t) cc_final: 0.8719 (m) REVERT: F 13 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8648 (mtpt) REVERT: F 127 HIS cc_start: 0.7294 (t-170) cc_final: 0.7008 (t-170) REVERT: F 277 PHE cc_start: 0.8793 (m-10) cc_final: 0.8561 (m-80) REVERT: F 278 MET cc_start: 0.8154 (tmm) cc_final: 0.7893 (tmm) REVERT: G 86 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7989 (mmm160) REVERT: G 88 GLU cc_start: 0.8647 (pt0) cc_final: 0.8431 (pt0) REVERT: G 349 PHE cc_start: 0.8594 (t80) cc_final: 0.8104 (t80) outliers start: 31 outliers final: 8 residues processed: 246 average time/residue: 0.0999 time to fit residues: 31.9381 Evaluate side-chains 185 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain F residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN B 27 ASN B 155 ASN F 15 GLN F 46 ASN F 116 ASN F 267 ASN G 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121709 restraints weight = 9684.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125503 restraints weight = 5338.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127983 restraints weight = 3739.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129389 restraints weight = 3030.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130439 restraints weight = 2667.509| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7663 Z= 0.123 Angle : 0.729 8.863 10389 Z= 0.377 Chirality : 0.043 0.366 1233 Planarity : 0.006 0.072 1292 Dihedral : 11.344 152.563 1075 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.88 % Favored : 88.02 % Rotamer: Outliers : 2.62 % Allowed : 18.43 % Favored : 78.95 % 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: -5.45 (0.21), residues: 943 helix: -3.53 (0.16), residues: 512 sheet: -1.35 (0.71), residues: 52 loop : -3.93 (0.26), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 136 TYR 0.023 0.001 TYR G 257 PHE 0.019 0.001 PHE F 69 TRP 0.013 0.001 TRP F 330 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7663) covalent geometry : angle 0.72938 / 0.38 (10389) hydrogen bonds : bond 0.03548 / 2.32 ( 233) hydrogen bonds : angle 5.90958 / 4.07 ( 666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8301 (mtm-85) REVERT: A 105 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7955 (mm) REVERT: A 157 LYS cc_start: 0.7938 (mttt) cc_final: 0.7657 (mttp) REVERT: A 183 LEU cc_start: 0.9336 (mt) cc_final: 0.8951 (mp) REVERT: A 198 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7327 (ttm110) REVERT: A 204 CYS cc_start: 0.8161 (m) cc_final: 0.7840 (m) REVERT: A 218 HIS cc_start: 0.7851 (t-170) cc_final: 0.7554 (t70) REVERT: B 86 GLU cc_start: 0.8018 (pm20) cc_final: 0.7791 (pm20) REVERT: B 155 ASN cc_start: 0.8490 (t0) cc_final: 0.8083 (t0) REVERT: B 197 VAL cc_start: 0.8726 (m) cc_final: 0.8520 (m) REVERT: B 223 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7194 (tm-30) REVERT: F 13 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8623 (mtpt) REVERT: F 127 HIS cc_start: 0.7095 (t-170) cc_final: 0.6876 (t-170) REVERT: F 279 MET cc_start: 0.8344 (tpp) cc_final: 0.8143 (tpp) REVERT: G 86 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7853 (mmm160) REVERT: G 88 GLU cc_start: 0.8656 (pt0) cc_final: 0.8408 (pt0) REVERT: G 122 GLU cc_start: 0.7951 (pp20) cc_final: 0.7729 (pp20) REVERT: G 131 MET cc_start: 0.7805 (ttt) cc_final: 0.7601 (ttm) outliers start: 21 outliers final: 14 residues processed: 204 average time/residue: 0.0930 time to fit residues: 25.1934 Evaluate side-chains 182 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN A 136 GLN B 27 ASN B 113 GLN F 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112148 restraints weight = 9964.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115670 restraints weight = 5740.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117932 restraints weight = 4115.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119382 restraints weight = 3372.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120192 restraints weight = 2979.383| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7663 Z= 0.156 Angle : 0.714 8.397 10389 Z= 0.360 Chirality : 0.043 0.244 1233 Planarity : 0.005 0.065 1292 Dihedral : 10.124 144.820 1065 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.09 % Favored : 87.80 % Rotamer: Outliers : 4.73 % Allowed : 21.05 % Favored : 74.22 % 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: -4.44 (0.24), residues: 943 helix: -2.61 (0.20), residues: 511 sheet: -1.16 (0.65), residues: 68 loop : -3.66 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.018 0.001 TYR G 257 PHE 0.020 0.002 PHE G 326 TRP 0.012 0.001 TRP F 123 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7663) covalent geometry : angle 0.71374 / 0.36 (10389) hydrogen bonds : bond 0.03304 / 2.18 ( 233) hydrogen bonds : angle 5.23822 / 3.58 ( 666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.280 Fit side-chains REVERT: A 155 ASN cc_start: 0.8598 (t0) cc_final: 0.8392 (t0) REVERT: A 157 LYS cc_start: 0.8127 (mttt) cc_final: 0.7912 (mttp) REVERT: A 198 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7274 (ttm110) REVERT: A 218 HIS cc_start: 0.7872 (t-170) cc_final: 0.7649 (t-90) REVERT: B 155 ASN cc_start: 0.8411 (t0) cc_final: 0.8102 (t0) REVERT: F 13 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8653 (mtpt) REVERT: G 86 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7876 (mmm160) REVERT: G 88 GLU cc_start: 0.8733 (pt0) cc_final: 0.8494 (pt0) REVERT: G 131 MET cc_start: 0.7944 (ttt) cc_final: 0.7738 (ttm) outliers start: 38 outliers final: 24 residues processed: 197 average time/residue: 0.1002 time to fit residues: 25.9103 Evaluate side-chains 185 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116781 restraints weight = 9886.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120419 restraints weight = 5623.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122862 restraints weight = 3983.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124186 restraints weight = 3215.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125327 restraints weight = 2838.466| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7663 Z= 0.121 Angle : 0.686 9.335 10389 Z= 0.342 Chirality : 0.043 0.366 1233 Planarity : 0.005 0.061 1292 Dihedral : 9.647 145.952 1059 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.49 % Allowed : 23.04 % Favored : 73.47 % 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: -3.97 (0.25), residues: 943 helix: -2.14 (0.21), residues: 518 sheet: -0.97 (0.65), residues: 74 loop : -3.65 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 17 TYR 0.019 0.001 TYR G 257 PHE 0.020 0.001 PHE G 326 TRP 0.007 0.001 TRP F 123 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7663) covalent geometry : angle 0.68616 / 0.34 (10389) hydrogen bonds : bond 0.02798 / 1.80 ( 233) hydrogen bonds : angle 4.91997 / 3.35 ( 666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8388 (mtm-85) REVERT: A 65 ASP cc_start: 0.7380 (m-30) cc_final: 0.7066 (m-30) REVERT: A 155 ASN cc_start: 0.8632 (t0) cc_final: 0.8347 (t0) REVERT: A 157 LYS cc_start: 0.7951 (mttt) cc_final: 0.7722 (mttp) REVERT: B 86 GLU cc_start: 0.8134 (pm20) cc_final: 0.7903 (pm20) REVERT: F 13 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8631 (mtpt) REVERT: F 98 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (pp) REVERT: F 338 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7180 (t80) REVERT: G 86 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7798 (mmm160) REVERT: G 131 MET cc_start: 0.7951 (ttt) cc_final: 0.7748 (ttm) outliers start: 28 outliers final: 17 residues processed: 182 average time/residue: 0.0933 time to fit residues: 22.4502 Evaluate side-chains 178 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131063 restraints weight = 9763.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135080 restraints weight = 5416.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137689 restraints weight = 3809.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139159 restraints weight = 3078.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140291 restraints weight = 2722.082| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7663 Z= 0.164 Angle : 0.727 14.981 10389 Z= 0.358 Chirality : 0.044 0.277 1233 Planarity : 0.005 0.061 1292 Dihedral : 9.073 143.599 1056 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.41 % Favored : 87.49 % Rotamer: Outliers : 4.98 % Allowed : 22.54 % Favored : 72.48 % 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: -3.74 (0.26), residues: 943 helix: -1.89 (0.21), residues: 524 sheet: -0.95 (0.64), residues: 74 loop : -3.66 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 198 TYR 0.016 0.001 TYR G 257 PHE 0.022 0.002 PHE G 326 TRP 0.008 0.001 TRP F 119 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 7663) covalent geometry : angle 0.72719 / 0.36 (10389) hydrogen bonds : bond 0.03004 / 1.98 ( 233) hydrogen bonds : angle 4.82088 / 3.27 ( 666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.277 Fit side-chains REVERT: A 14 LYS cc_start: 0.8530 (tppt) cc_final: 0.8016 (mmtm) REVERT: A 65 ASP cc_start: 0.7297 (m-30) cc_final: 0.7049 (m-30) REVERT: A 155 ASN cc_start: 0.8677 (t0) cc_final: 0.8349 (t0) REVERT: A 198 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7390 (ttm170) REVERT: A 218 HIS cc_start: 0.7821 (t-170) cc_final: 0.7502 (t70) REVERT: A 239 PHE cc_start: 0.6153 (t80) cc_final: 0.5769 (t80) REVERT: B 86 GLU cc_start: 0.8188 (pm20) cc_final: 0.7848 (pm20) REVERT: B 157 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7384 (mttp) REVERT: B 198 ARG cc_start: 0.7391 (ttt90) cc_final: 0.6978 (tmm-80) REVERT: F 13 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8558 (mtpt) REVERT: F 278 MET cc_start: 0.8083 (ppp) cc_final: 0.7845 (tmm) REVERT: F 338 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.6523 (t80) REVERT: G 86 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7880 (mmm160) REVERT: G 131 MET cc_start: 0.7927 (ttt) cc_final: 0.7713 (ttm) outliers start: 40 outliers final: 20 residues processed: 186 average time/residue: 0.0939 time to fit residues: 23.0822 Evaluate side-chains 179 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122632 restraints weight = 9844.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126605 restraints weight = 5422.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129185 restraints weight = 3783.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130648 restraints weight = 3042.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131728 restraints weight = 2679.334| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7663 Z= 0.178 Angle : 0.750 14.773 10389 Z= 0.369 Chirality : 0.044 0.236 1233 Planarity : 0.005 0.062 1292 Dihedral : 9.018 141.784 1055 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.20 % Favored : 87.70 % Rotamer: Outliers : 3.99 % Allowed : 24.66 % Favored : 71.36 % 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: -3.55 (0.26), residues: 943 helix: -1.74 (0.22), residues: 524 sheet: -1.02 (0.64), residues: 74 loop : -3.54 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.020 0.002 TYR G 257 PHE 0.018 0.002 PHE G 326 TRP 0.013 0.001 TRP F 123 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 7663) covalent geometry : angle 0.74995 / 0.37 (10389) hydrogen bonds : bond 0.03064 / 2.02 ( 233) hydrogen bonds : angle 4.82299 / 3.26 ( 666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8604 (tppt) cc_final: 0.8115 (mmtm) REVERT: A 17 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8405 (mtm-85) REVERT: A 65 ASP cc_start: 0.7352 (m-30) cc_final: 0.7120 (m-30) REVERT: A 155 ASN cc_start: 0.8659 (t0) cc_final: 0.8318 (t0) REVERT: A 198 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7422 (mmm-85) REVERT: A 218 HIS cc_start: 0.7851 (t-170) cc_final: 0.7544 (t70) REVERT: A 239 PHE cc_start: 0.6240 (t80) cc_final: 0.5907 (t80) REVERT: B 86 GLU cc_start: 0.8216 (pm20) cc_final: 0.7979 (pm20) REVERT: F 278 MET cc_start: 0.8042 (ppp) cc_final: 0.7698 (tmm) REVERT: F 303 MET cc_start: 0.7579 (tpt) cc_final: 0.7301 (mmm) REVERT: F 338 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.6468 (t80) REVERT: G 86 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7840 (mmm160) REVERT: G 131 MET cc_start: 0.7952 (ttt) cc_final: 0.7558 (ttm) REVERT: G 257 TYR cc_start: 0.7238 (t80) cc_final: 0.7004 (t80) outliers start: 32 outliers final: 23 residues processed: 176 average time/residue: 0.0990 time to fit residues: 23.0259 Evaluate side-chains 173 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123034 restraints weight = 9803.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126753 restraints weight = 5672.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129154 restraints weight = 4064.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130581 restraints weight = 3325.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131647 restraints weight = 2941.029| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7663 Z= 0.126 Angle : 0.708 12.976 10389 Z= 0.346 Chirality : 0.044 0.382 1233 Planarity : 0.004 0.057 1292 Dihedral : 8.845 142.549 1055 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.41 % Favored : 87.49 % Rotamer: Outliers : 3.36 % Allowed : 24.91 % Favored : 71.73 % 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: -3.24 (0.27), residues: 943 helix: -1.43 (0.22), residues: 522 sheet: -0.89 (0.64), residues: 74 loop : -3.49 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.018 0.001 TYR G 257 PHE 0.015 0.001 PHE G 326 TRP 0.014 0.001 TRP F 123 HIS 0.003 0.001 HIS F 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7663) covalent geometry : angle 0.70763 / 0.35 (10389) hydrogen bonds : bond 0.02700 / 1.74 ( 233) hydrogen bonds : angle 4.69039 / 3.15 ( 666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8633 (tppt) cc_final: 0.8166 (mmtm) REVERT: A 17 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8503 (mtm-85) REVERT: A 155 ASN cc_start: 0.8692 (t0) cc_final: 0.8336 (t0) REVERT: A 198 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7422 (mmm-85) REVERT: A 218 HIS cc_start: 0.7858 (t-170) cc_final: 0.7590 (t70) REVERT: B 7 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8225 (ttmm) REVERT: B 86 GLU cc_start: 0.8186 (pm20) cc_final: 0.7801 (pm20) REVERT: B 155 ASN cc_start: 0.8706 (t0) cc_final: 0.8458 (t0) REVERT: F 127 HIS cc_start: 0.7020 (t-90) cc_final: 0.6817 (t-90) REVERT: F 278 MET cc_start: 0.7988 (ppp) cc_final: 0.7631 (tmm) REVERT: F 338 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6278 (t80) REVERT: G 21 MET cc_start: 0.7814 (tpp) cc_final: 0.7554 (tpt) REVERT: G 86 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7709 (mmm160) REVERT: G 131 MET cc_start: 0.7893 (ttt) cc_final: 0.7528 (ttm) REVERT: G 257 TYR cc_start: 0.7129 (t80) cc_final: 0.6823 (t80) outliers start: 27 outliers final: 18 residues processed: 173 average time/residue: 0.0954 time to fit residues: 21.8060 Evaluate side-chains 171 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127978 restraints weight = 9683.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131936 restraints weight = 5361.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134525 restraints weight = 3750.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136135 restraints weight = 3016.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137150 restraints weight = 2640.189| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7663 Z= 0.153 Angle : 0.714 12.239 10389 Z= 0.350 Chirality : 0.044 0.357 1233 Planarity : 0.004 0.059 1292 Dihedral : 8.765 141.027 1055 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.30 % Favored : 87.59 % Rotamer: Outliers : 3.61 % Allowed : 25.28 % Favored : 71.11 % 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: -3.11 (0.27), residues: 943 helix: -1.30 (0.22), residues: 528 sheet: -1.01 (0.64), residues: 74 loop : -3.46 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.017 0.001 TYR G 257 PHE 0.015 0.001 PHE F 69 TRP 0.016 0.001 TRP F 123 HIS 0.003 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7663) covalent geometry : angle 0.71447 / 0.35 (10389) hydrogen bonds : bond 0.02814 / 1.84 ( 233) hydrogen bonds : angle 4.69609 / 3.15 ( 666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8660 (tppt) cc_final: 0.8219 (mmtm) REVERT: A 17 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8374 (mtm-85) REVERT: A 105 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8373 (mm) REVERT: A 155 ASN cc_start: 0.8761 (t0) cc_final: 0.8419 (t0) REVERT: A 198 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7188 (ttm170) REVERT: A 218 HIS cc_start: 0.7902 (t-170) cc_final: 0.7612 (t70) REVERT: B 7 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8248 (ttmm) REVERT: B 86 GLU cc_start: 0.8219 (pm20) cc_final: 0.7862 (pm20) REVERT: B 155 ASN cc_start: 0.8621 (t0) cc_final: 0.8240 (t0) REVERT: B 198 ARG cc_start: 0.7423 (ttt90) cc_final: 0.6900 (tmm-80) REVERT: F 278 MET cc_start: 0.8012 (ppp) cc_final: 0.7591 (tmm) REVERT: F 338 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6251 (t80) REVERT: G 21 MET cc_start: 0.7791 (tpp) cc_final: 0.7561 (tpt) REVERT: G 86 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7675 (mmm160) REVERT: G 131 MET cc_start: 0.7870 (ttt) cc_final: 0.7504 (ttm) outliers start: 29 outliers final: 21 residues processed: 170 average time/residue: 0.0878 time to fit residues: 20.1368 Evaluate side-chains 171 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.0670 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124605 restraints weight = 9708.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128412 restraints weight = 5564.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130903 restraints weight = 3979.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132312 restraints weight = 3240.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133265 restraints weight = 2866.401| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7663 Z= 0.101 Angle : 0.664 12.054 10389 Z= 0.325 Chirality : 0.042 0.348 1233 Planarity : 0.004 0.054 1292 Dihedral : 8.522 142.247 1055 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 1.87 % Allowed : 27.52 % Favored : 70.61 % 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: -2.63 (0.28), residues: 943 helix: -0.89 (0.23), residues: 516 sheet: -0.75 (0.66), residues: 72 loop : -3.24 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.016 0.001 TYR G 257 PHE 0.019 0.001 PHE G 326 TRP 0.023 0.001 TRP F 123 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7663) covalent geometry : angle 0.66375 / 0.32 (10389) hydrogen bonds : bond 0.02450 / 1.58 ( 233) hydrogen bonds : angle 4.51260 / 3.01 ( 666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.285 Fit side-chains REVERT: A 14 LYS cc_start: 0.8390 (tppt) cc_final: 0.7965 (mmtm) REVERT: A 86 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: A 105 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 155 ASN cc_start: 0.8632 (t0) cc_final: 0.8301 (t0) REVERT: A 198 ARG cc_start: 0.7485 (ttm110) cc_final: 0.6486 (mmm-85) REVERT: A 218 HIS cc_start: 0.7716 (t-170) cc_final: 0.7508 (t70) REVERT: B 86 GLU cc_start: 0.8139 (pm20) cc_final: 0.7848 (pm20) REVERT: B 155 ASN cc_start: 0.8640 (t0) cc_final: 0.8287 (t0) REVERT: B 198 ARG cc_start: 0.7252 (ttt90) cc_final: 0.6906 (tmm-80) REVERT: F 13 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8493 (mtpt) REVERT: F 278 MET cc_start: 0.7944 (ppp) cc_final: 0.7721 (tmm) REVERT: F 338 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6569 (t80) REVERT: G 86 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7769 (mmm160) REVERT: G 131 MET cc_start: 0.7957 (ttt) cc_final: 0.7740 (ttm) outliers start: 15 outliers final: 10 residues processed: 178 average time/residue: 0.0971 time to fit residues: 22.9168 Evaluate side-chains 170 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122291 restraints weight = 9708.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126098 restraints weight = 5443.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128553 restraints weight = 3842.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129934 restraints weight = 3123.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130887 restraints weight = 2770.116| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 7663 Z= 0.284 Angle : 0.829 11.780 10389 Z= 0.409 Chirality : 0.050 0.332 1233 Planarity : 0.005 0.070 1292 Dihedral : 8.845 138.865 1055 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.10 % Favored : 85.79 % Rotamer: Outliers : 2.62 % Allowed : 26.53 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.27), residues: 943 helix: -1.25 (0.23), residues: 510 sheet: -1.18 (0.64), residues: 74 loop : -3.28 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 198 TYR 0.018 0.002 TYR F 6 PHE 0.020 0.002 PHE F 69 TRP 0.022 0.002 TRP F 123 HIS 0.007 0.001 HIS F 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.28 ( 7663) covalent geometry : angle 0.82926 / 0.41 (10389) hydrogen bonds : bond 0.03514 / 2.38 ( 233) hydrogen bonds : angle 4.93479 / 3.33 ( 666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8598 (tppt) cc_final: 0.8151 (mmtm) REVERT: A 105 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 155 ASN cc_start: 0.8672 (t0) cc_final: 0.8350 (t0) REVERT: A 198 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7451 (ttm170) REVERT: A 218 HIS cc_start: 0.7897 (t-170) cc_final: 0.7648 (t70) REVERT: B 86 GLU cc_start: 0.8331 (pm20) cc_final: 0.8020 (pm20) REVERT: B 155 ASN cc_start: 0.8666 (t0) cc_final: 0.8287 (t0) REVERT: F 278 MET cc_start: 0.8091 (ppp) cc_final: 0.7768 (tmm) REVERT: F 338 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.6257 (t80) REVERT: G 21 MET cc_start: 0.7818 (tpp) cc_final: 0.7577 (tpt) REVERT: G 86 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7834 (mmm160) REVERT: G 131 MET cc_start: 0.7937 (ttt) cc_final: 0.7549 (ttm) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.0973 time to fit residues: 21.2780 Evaluate side-chains 163 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124857 restraints weight = 9618.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128545 restraints weight = 5530.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130994 restraints weight = 3967.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132383 restraints weight = 3236.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133193 restraints weight = 2864.465| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7663 Z= 0.110 Angle : 0.698 11.742 10389 Z= 0.341 Chirality : 0.044 0.341 1233 Planarity : 0.004 0.068 1292 Dihedral : 8.621 141.291 1055 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 1.37 % Allowed : 27.65 % Favored : 70.98 % 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: -2.66 (0.27), residues: 943 helix: -0.87 (0.23), residues: 513 sheet: -0.95 (0.65), residues: 74 loop : -3.27 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 133 TYR 0.015 0.001 TYR G 257 PHE 0.015 0.001 PHE G 326 TRP 0.026 0.001 TRP F 123 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7663) covalent geometry : angle 0.69752 / 0.34 (10389) hydrogen bonds : bond 0.02569 / 1.64 ( 233) hydrogen bonds : angle 4.62225 / 3.08 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.55 seconds wall clock time: 24 minutes 30.41 seconds (1470.41 seconds total)