Starting phenix.real_space_refine on Wed Mar 4 03:10:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8g_10121/03_2026/6s8g_10121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8g_10121/03_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_10121/03_2026/6s8g_10121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8g_10121/03_2026/6s8g_10121.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8g_10121/03_2026/6s8g_10121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8g_10121/03_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-dev-5986/lib/python3.9/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: 28 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.86, per 1000 atoms: 0.25 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: 0.84 Conformation dependent library (CDL) restraints added in 189.4 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: 0.22 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: 1.01 Time building geometry restraints manager: 1.03 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: 4214 23.00 - 46.00: 355 46.00 - 69.01: 69 69.01 - 92.01: 21 92.01 - 115.01: 4 Dihedral angle restraints: 4663 sinusoidal: 1921 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 4660 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 18.450 115.010 2895 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 covalent geometry : bond 0.00974 ( 7663) covalent geometry : angle 1.32290 (10389) hydrogen bonds : bond 0.29925 ( 233) hydrogen bonds : angle 11.19427 ( 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 : 0.261 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: 0.1031 time to fit residues: 32.5090 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 : 0.254 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3695 r_free = 0.3695 target = 0.148934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121322 restraints weight = 9732.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124599 restraints weight = 5825.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126781 restraints weight = 4274.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128079 restraints weight = 3531.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128979 restraints weight = 3135.414| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7663 Z= 0.126 Angle : 0.746 9.031 10389 Z= 0.381 Chirality : 0.044 0.371 1233 Planarity : 0.006 0.072 1292 Dihedral : 13.596 148.449 1155 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.09 % Favored : 87.80 % Rotamer: Outliers : 2.62 % Allowed : 18.93 % Favored : 78.46 % 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: -5.46 (0.21), residues: 943 helix: -3.55 (0.16), residues: 508 sheet: -1.36 (0.71), residues: 52 loop : -3.93 (0.26), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.023 0.001 TYR G 257 PHE 0.019 0.001 PHE F 69 TRP 0.012 0.002 TRP F 123 HIS 0.006 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7663) covalent geometry : angle 0.74635 (10389) hydrogen bonds : bond 0.03744 ( 233) hydrogen bonds : angle 5.97367 ( 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 211 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 157 LYS cc_start: 0.8027 (mttt) cc_final: 0.7762 (mttp) REVERT: A 183 LEU cc_start: 0.9397 (mt) cc_final: 0.9029 (mp) REVERT: A 198 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7163 (ttm110) REVERT: A 204 CYS cc_start: 0.8046 (m) cc_final: 0.7700 (m) REVERT: A 218 HIS cc_start: 0.7692 (t-170) cc_final: 0.7458 (t70) REVERT: B 155 ASN cc_start: 0.8427 (t0) cc_final: 0.8062 (t0) REVERT: B 198 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7116 (ttp80) REVERT: B 223 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7201 (tm-30) REVERT: F 13 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8597 (mtpt) REVERT: F 279 MET cc_start: 0.8226 (tpp) cc_final: 0.8011 (tpp) REVERT: G 140 MET cc_start: 0.4765 (mtm) cc_final: 0.4558 (mtm) outliers start: 21 outliers final: 14 residues processed: 203 average time/residue: 0.0955 time to fit residues: 25.5437 Evaluate side-chains 180 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 136 GLN B 27 ASN B 113 GLN F 127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121394 restraints weight = 9739.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124750 restraints weight = 5812.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126949 restraints weight = 4242.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128328 restraints weight = 3491.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128890 restraints weight = 3092.331| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7663 Z= 0.114 Angle : 0.690 8.248 10389 Z= 0.347 Chirality : 0.042 0.255 1233 Planarity : 0.005 0.062 1292 Dihedral : 11.401 147.190 1145 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 3.36 % Allowed : 21.54 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.24), residues: 943 helix: -2.62 (0.20), residues: 512 sheet: -1.04 (0.67), residues: 68 loop : -3.71 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.017 0.001 TYR G 257 PHE 0.022 0.001 PHE G 326 TRP 0.011 0.001 TRP F 123 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7663) covalent geometry : angle 0.69001 (10389) hydrogen bonds : bond 0.02950 ( 233) hydrogen bonds : angle 5.16762 ( 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 199 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 204 CYS cc_start: 0.7989 (m) cc_final: 0.7691 (m) REVERT: B 155 ASN cc_start: 0.8310 (t0) cc_final: 0.8055 (t0) REVERT: F 13 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8602 (mtpt) REVERT: F 127 HIS cc_start: 0.6943 (t-90) cc_final: 0.6729 (t-90) REVERT: G 140 MET cc_start: 0.4646 (mtm) cc_final: 0.4440 (mtm) outliers start: 27 outliers final: 17 residues processed: 187 average time/residue: 0.0946 time to fit residues: 23.2345 Evaluate side-chains 179 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114093 restraints weight = 10056.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117471 restraints weight = 6001.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119728 restraints weight = 4368.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121052 restraints weight = 3587.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121901 restraints weight = 3178.448| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7663 Z= 0.148 Angle : 0.715 15.494 10389 Z= 0.351 Chirality : 0.044 0.363 1233 Planarity : 0.005 0.063 1292 Dihedral : 10.428 149.539 1139 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.62 % Favored : 87.27 % Rotamer: Outliers : 3.99 % Allowed : 21.79 % 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: -3.99 (0.25), residues: 943 helix: -2.14 (0.21), residues: 524 sheet: -0.96 (0.65), residues: 74 loop : -3.72 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 198 TYR 0.019 0.001 TYR G 257 PHE 0.022 0.001 PHE G 326 TRP 0.014 0.001 TRP F 123 HIS 0.004 0.001 HIS F 89 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7663) covalent geometry : angle 0.71541 (10389) hydrogen bonds : bond 0.03006 ( 233) hydrogen bonds : angle 4.93924 ( 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 198 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.231 Fit side-chains REVERT: A 155 ASN cc_start: 0.8576 (t0) cc_final: 0.8306 (t0) REVERT: A 198 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7421 (ttm170) REVERT: B 198 ARG cc_start: 0.7391 (ttt90) cc_final: 0.7091 (tmm-80) REVERT: F 13 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8604 (mtpt) REVERT: F 98 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8520 (pp) REVERT: F 338 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7448 (t80) REVERT: G 283 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8788 (tp) outliers start: 32 outliers final: 18 residues processed: 184 average time/residue: 0.1007 time to fit residues: 24.1965 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 : 0.296 ------------------------------------------------------------------------------- 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 123 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 98 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 277 PHE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 283 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS F 127 HIS G 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130449 restraints weight = 9654.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134311 restraints weight = 5372.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136851 restraints weight = 3774.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138403 restraints weight = 3043.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139229 restraints weight = 2671.197| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7663 Z= 0.136 Angle : 0.696 12.257 10389 Z= 0.344 Chirality : 0.044 0.289 1233 Planarity : 0.004 0.059 1292 Dihedral : 9.834 153.430 1136 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.09 % Favored : 87.80 % Rotamer: Outliers : 3.99 % Allowed : 22.79 % Favored : 73.23 % 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: -3.63 (0.26), residues: 943 helix: -1.83 (0.22), residues: 524 sheet: -0.79 (0.67), residues: 74 loop : -3.61 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.019 0.001 TYR G 257 PHE 0.021 0.001 PHE G 326 TRP 0.007 0.001 TRP F 123 HIS 0.003 0.001 HIS F 89 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7663) covalent geometry : angle 0.69585 (10389) hydrogen bonds : bond 0.02821 ( 233) hydrogen bonds : angle 4.76052 ( 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 195 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.212 Fit side-chains REVERT: A 17 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8461 (mtm-85) REVERT: A 65 ASP cc_start: 0.7383 (m-30) cc_final: 0.7058 (m-30) REVERT: A 155 ASN cc_start: 0.8688 (t0) cc_final: 0.8373 (t0) REVERT: A 198 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7363 (ttm170) REVERT: A 239 PHE cc_start: 0.6055 (t80) cc_final: 0.5612 (t80) REVERT: B 97 ASP cc_start: 0.8042 (m-30) cc_final: 0.7718 (m-30) REVERT: B 157 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7398 (mttp) REVERT: B 198 ARG cc_start: 0.7493 (ttt90) cc_final: 0.6978 (tmm-80) REVERT: F 13 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8544 (mtpt) REVERT: F 98 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8471 (pp) REVERT: F 127 HIS cc_start: 0.7254 (t-90) cc_final: 0.6983 (t-90) REVERT: F 265 GLU cc_start: 0.8768 (mp0) cc_final: 0.8518 (mp0) REVERT: F 338 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7246 (t80) REVERT: G 140 MET cc_start: 0.4641 (mtm) cc_final: 0.4356 (mtm) REVERT: G 283 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8702 (tp) outliers start: 32 outliers final: 20 residues processed: 181 average time/residue: 0.0974 time to fit residues: 23.0726 Evaluate side-chains 181 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 97 VAL 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 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 283 LEU 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 348 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 59 optimal weight: 0.0060 chunk 55 optimal weight: 0.1980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131962 restraints weight = 9695.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135874 restraints weight = 5433.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138297 restraints weight = 3821.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139925 restraints weight = 3105.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140759 restraints weight = 2715.781| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7663 Z= 0.118 Angle : 0.685 12.115 10389 Z= 0.337 Chirality : 0.042 0.246 1233 Planarity : 0.004 0.057 1292 Dihedral : 9.832 159.448 1136 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 3.74 % Allowed : 24.03 % Favored : 72.23 % 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: -3.28 (0.27), residues: 943 helix: -1.50 (0.22), residues: 520 sheet: -0.68 (0.68), residues: 74 loop : -3.50 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 270 TYR 0.015 0.001 TYR G 257 PHE 0.024 0.001 PHE G 326 TRP 0.007 0.001 TRP F 123 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7663) covalent geometry : angle 0.68472 (10389) hydrogen bonds : bond 0.02651 ( 233) hydrogen bonds : angle 4.68720 ( 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 190 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8403 (tppt) cc_final: 0.7889 (mmtm) REVERT: A 17 ARG cc_start: 0.8736 (mtp85) cc_final: 0.8527 (mtm-85) REVERT: A 155 ASN cc_start: 0.8563 (t0) cc_final: 0.8240 (t0) REVERT: A 198 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7224 (ttm170) REVERT: A 239 PHE cc_start: 0.6206 (t80) cc_final: 0.5761 (t80) REVERT: B 155 ASN cc_start: 0.8632 (t0) cc_final: 0.8429 (t0) REVERT: B 198 ARG cc_start: 0.7285 (ttt90) cc_final: 0.6895 (tmm-80) REVERT: F 13 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8518 (mtpt) REVERT: F 338 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7080 (t80) REVERT: G 283 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (tp) outliers start: 30 outliers final: 15 residues processed: 177 average time/residue: 0.0819 time to fit residues: 19.3298 Evaluate side-chains 173 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 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 99 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN F 127 HIS G 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129821 restraints weight = 9697.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133764 restraints weight = 5369.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136371 restraints weight = 3727.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137985 restraints weight = 2990.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138837 restraints weight = 2613.484| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7663 Z= 0.144 Angle : 0.703 11.084 10389 Z= 0.343 Chirality : 0.044 0.387 1233 Planarity : 0.004 0.066 1292 Dihedral : 9.853 163.197 1135 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.66 % Favored : 88.23 % Rotamer: Outliers : 3.61 % Allowed : 24.28 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.27), residues: 943 helix: -1.41 (0.22), residues: 522 sheet: -0.83 (0.66), residues: 74 loop : -3.46 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 133 TYR 0.015 0.001 TYR G 257 PHE 0.025 0.001 PHE G 326 TRP 0.006 0.001 TRP F 123 HIS 0.003 0.001 HIS F 89 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7663) covalent geometry : angle 0.70346 (10389) hydrogen bonds : bond 0.02824 ( 233) hydrogen bonds : angle 4.72923 ( 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 185 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8563 (tppt) cc_final: 0.8049 (mmtm) REVERT: A 17 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8518 (mtm-85) REVERT: A 105 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 155 ASN cc_start: 0.8703 (t0) cc_final: 0.8363 (t0) REVERT: A 181 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 198 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7173 (ttm170) REVERT: A 239 PHE cc_start: 0.6224 (t80) cc_final: 0.5860 (t80) REVERT: B 97 ASP cc_start: 0.8004 (m-30) cc_final: 0.7751 (m-30) REVERT: B 155 ASN cc_start: 0.8644 (t0) cc_final: 0.8296 (t0) REVERT: B 188 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7447 (tp) REVERT: B 198 ARG cc_start: 0.7445 (ttt90) cc_final: 0.6891 (tmm-80) REVERT: F 13 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8489 (mtpt) REVERT: F 127 HIS cc_start: 0.7041 (t-90) cc_final: 0.6806 (t-90) REVERT: F 338 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7151 (t80) REVERT: G 283 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8585 (tp) outliers start: 29 outliers final: 21 residues processed: 170 average time/residue: 0.0997 time to fit residues: 22.1082 Evaluate side-chains 180 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 188 LEU 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 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 283 LEU Chi-restraints excluded: chain G residue 293 LEU 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: 0.9980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 62 optimal weight: 0.0370 chunk 73 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN G 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123335 restraints weight = 9759.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127249 restraints weight = 5439.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129843 restraints weight = 3833.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131249 restraints weight = 3090.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132430 restraints weight = 2730.328| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7663 Z= 0.104 Angle : 0.665 10.801 10389 Z= 0.324 Chirality : 0.043 0.375 1233 Planarity : 0.004 0.063 1292 Dihedral : 9.940 172.503 1135 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 3.11 % Allowed : 25.03 % Favored : 71.86 % 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: -2.84 (0.27), residues: 943 helix: -1.11 (0.23), residues: 521 sheet: -0.67 (0.67), residues: 74 loop : -3.33 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 133 TYR 0.020 0.001 TYR G 257 PHE 0.025 0.001 PHE G 326 TRP 0.008 0.001 TRP F 123 HIS 0.003 0.000 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7663) covalent geometry : angle 0.66466 (10389) hydrogen bonds : bond 0.02542 ( 233) hydrogen bonds : angle 4.61455 ( 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 186 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8581 (tppt) cc_final: 0.8090 (mmtm) REVERT: A 17 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8480 (mtm-85) REVERT: A 105 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 155 ASN cc_start: 0.8704 (t0) cc_final: 0.8332 (t0) REVERT: A 181 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 198 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7290 (ttm170) REVERT: A 239 PHE cc_start: 0.6171 (t80) cc_final: 0.5939 (t80) REVERT: B 86 GLU cc_start: 0.8187 (pm20) cc_final: 0.7953 (pm20) REVERT: B 97 ASP cc_start: 0.7973 (m-30) cc_final: 0.7724 (m-30) REVERT: B 155 ASN cc_start: 0.8619 (t0) cc_final: 0.8228 (t0) REVERT: B 198 ARG cc_start: 0.7459 (ttt90) cc_final: 0.6962 (tmm-80) REVERT: F 13 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8448 (mtpt) REVERT: F 251 MET cc_start: 0.7496 (mmt) cc_final: 0.7200 (mmp) REVERT: F 338 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7033 (t80) REVERT: G 283 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8467 (tt) outliers start: 25 outliers final: 19 residues processed: 176 average time/residue: 0.0985 time to fit residues: 22.6951 Evaluate side-chains 177 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 86 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 GLU 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 B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 284 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 283 LEU 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: 0.7980 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132237 restraints weight = 9589.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135874 restraints weight = 5509.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138297 restraints weight = 3953.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139725 restraints weight = 3213.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140420 restraints weight = 2832.545| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7663 Z= 0.103 Angle : 0.659 10.354 10389 Z= 0.321 Chirality : 0.043 0.366 1233 Planarity : 0.004 0.061 1292 Dihedral : 9.933 176.774 1135 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 3.11 % Allowed : 25.40 % Favored : 71.48 % 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: -2.57 (0.27), residues: 943 helix: -0.81 (0.23), residues: 519 sheet: -0.60 (0.69), residues: 72 loop : -3.32 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 133 TYR 0.018 0.001 TYR G 257 PHE 0.024 0.001 PHE G 326 TRP 0.008 0.001 TRP F 123 HIS 0.003 0.000 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7663) covalent geometry : angle 0.65940 (10389) hydrogen bonds : bond 0.02498 ( 233) hydrogen bonds : angle 4.55835 ( 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 180 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8449 (tppt) cc_final: 0.7982 (mmtm) REVERT: A 17 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8471 (mtm-85) REVERT: A 105 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 155 ASN cc_start: 0.8652 (t0) cc_final: 0.8322 (t0) REVERT: A 181 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 198 ARG cc_start: 0.7578 (ttm110) cc_final: 0.7099 (mmm-85) REVERT: A 239 PHE cc_start: 0.6213 (t80) cc_final: 0.5961 (t80) REVERT: B 86 GLU cc_start: 0.8148 (pm20) cc_final: 0.7945 (pm20) REVERT: B 97 ASP cc_start: 0.7826 (m-30) cc_final: 0.7618 (m-30) REVERT: B 155 ASN cc_start: 0.8657 (t0) cc_final: 0.8272 (t0) REVERT: B 198 ARG cc_start: 0.7395 (ttt90) cc_final: 0.6897 (tmm-80) REVERT: F 13 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8441 (mtpt) REVERT: F 57 PRO cc_start: 0.8916 (Cg_exo) cc_final: 0.8663 (Cg_endo) REVERT: F 251 MET cc_start: 0.7470 (mmt) cc_final: 0.7154 (mmp) REVERT: F 282 MET cc_start: 0.8800 (tpp) cc_final: 0.8267 (ttt) REVERT: F 338 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7844 (t80) outliers start: 25 outliers final: 16 residues processed: 171 average time/residue: 0.0860 time to fit residues: 19.4909 Evaluate side-chains 170 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 GLU 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 B residue 230 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 277 PHE 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 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: 8.9990 chunk 89 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.0000 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133779 restraints weight = 9530.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137821 restraints weight = 5247.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140345 restraints weight = 3635.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142143 restraints weight = 2912.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142756 restraints weight = 2521.764| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7663 Z= 0.098 Angle : 0.656 10.518 10389 Z= 0.318 Chirality : 0.043 0.365 1233 Planarity : 0.004 0.055 1292 Dihedral : 9.920 179.864 1135 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 1.87 % Allowed : 26.77 % 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: -2.28 (0.28), residues: 943 helix: -0.55 (0.24), residues: 523 sheet: -0.54 (0.71), residues: 70 loop : -3.21 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 133 TYR 0.019 0.001 TYR G 257 PHE 0.024 0.001 PHE G 326 TRP 0.009 0.001 TRP F 123 HIS 0.002 0.000 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7663) covalent geometry : angle 0.65629 (10389) hydrogen bonds : bond 0.02381 ( 233) hydrogen bonds : angle 4.48937 ( 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 177 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.310 Fit side-chains REVERT: A 14 LYS cc_start: 0.8369 (tppt) cc_final: 0.7919 (mmtm) REVERT: A 17 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8518 (mtm-85) REVERT: A 105 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 155 ASN cc_start: 0.8644 (t0) cc_final: 0.8331 (t0) REVERT: A 181 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: A 198 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7032 (mmm-85) REVERT: A 239 PHE cc_start: 0.6263 (t80) cc_final: 0.6016 (t80) REVERT: B 155 ASN cc_start: 0.8584 (t0) cc_final: 0.8217 (t0) REVERT: B 198 ARG cc_start: 0.7344 (ttt90) cc_final: 0.6873 (tmm-80) REVERT: B 231 LYS cc_start: 0.8698 (mttt) cc_final: 0.8430 (mttp) REVERT: F 13 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8458 (mtpt) REVERT: F 57 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: F 251 MET cc_start: 0.7446 (mmt) cc_final: 0.7160 (mmp) REVERT: F 282 MET cc_start: 0.8724 (tpp) cc_final: 0.8180 (ttt) REVERT: F 338 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7897 (t80) outliers start: 15 outliers final: 11 residues processed: 172 average time/residue: 0.0995 time to fit residues: 22.5828 Evaluate side-chains 170 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 181 GLU Chi-restraints excluded: chain B residue 3 THR 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 99 VAL Chi-restraints excluded: chain F residue 277 PHE 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 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 0.0570 chunk 4 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127106 restraints weight = 9645.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130827 restraints weight = 5627.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133337 restraints weight = 4037.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134826 restraints weight = 3280.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135902 restraints weight = 2886.640| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7663 Z= 0.102 Angle : 0.657 10.289 10389 Z= 0.320 Chirality : 0.043 0.354 1233 Planarity : 0.004 0.054 1292 Dihedral : 9.833 179.765 1134 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 1.87 % Allowed : 26.90 % Favored : 71.23 % 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: -2.16 (0.28), residues: 943 helix: -0.40 (0.24), residues: 521 sheet: -0.63 (0.73), residues: 67 loop : -3.19 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 133 TYR 0.018 0.001 TYR G 257 PHE 0.023 0.001 PHE G 326 TRP 0.008 0.001 TRP F 123 HIS 0.002 0.000 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7663) covalent geometry : angle 0.65733 (10389) hydrogen bonds : bond 0.02421 ( 233) hydrogen bonds : angle 4.46017 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1339.16 seconds wall clock time: 23 minutes 38.40 seconds (1418.40 seconds total)