Starting phenix.real_space_refine on Fri Jul 3 16:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzw_26920/07_2026/7uzw_26920.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 32 5.16 5 C 9199 2.51 5 N 2538 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1458 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain breaks: 2 Chain: "H" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2355 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3886 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 5, 'TRANS': 472} Chain breaks: 6 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 11, 'rna3p': 19} Time building chain proxies: 3.51, per 1000 atoms: 0.24 Number of scatterers: 14754 At special positions: 0 Unit cell: (92.4, 119.9, 203.5, 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 32 16.00 P 31 15.00 O 2954 8.00 N 2538 7.00 C 9199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 657.5 milliseconds 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 21 sheets defined 39.8% alpha, 21.1% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.844A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.629A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.899A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.996A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.630A pdb=" N ARG C 187 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.689A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'E' and resid 47 through 63 removed outlier: 3.753A pdb=" N ILE E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 76 through 83 Processing helix chain 'E' and resid 104 through 115 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 50 through 55 removed outlier: 3.959A pdb=" N ASN H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.504A pdb=" N LEU H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 228 through 236 removed outlier: 4.446A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.872A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.175A pdb=" N SER F 29 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.935A pdb=" N TYR F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.857A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 154 through 170 Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 205 through 227 removed outlier: 3.614A pdb=" N HIS F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.525A pdb=" N GLN F 248 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 279 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.784A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 386 removed outlier: 4.263A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 423 through 437 Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.680A pdb=" N THR F 539 " --> pdb=" O ASN F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 567 removed outlier: 3.634A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 574 Processing helix chain 'F' and resid 595 through 612 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.148A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER A 3 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS A 4 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR A 10 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP A 196 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 14 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE A 192 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 127 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.539A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.454A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.750A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.750A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.190A pdb=" N VAL D 151 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA D 101 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP D 149 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 103 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU D 147 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.203A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER E 8 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR E 197 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.990A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS E 4 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 71 " --> pdb=" O PRO H 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AB7, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'H' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.591A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'F' and resid 307 through 311 removed outlier: 5.899A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.958A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4805 1.34 - 1.47: 3719 1.47 - 1.60: 6459 1.60 - 1.73: 33 1.73 - 1.85: 57 Bond restraints: 15073 Sorted by residual: bond pdb=" C1' U G 24 " pdb=" N1 U G 24 " ideal model delta sigma weight residual 1.480 1.563 -0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.41e-02 5.03e+03 5.99e+00 bond pdb=" N ARG D 137 " pdb=" CA ARG D 137 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" CB CYS F 214 " pdb=" SG CYS F 214 " ideal model delta sigma weight residual 1.808 1.738 0.070 3.30e-02 9.18e+02 4.54e+00 ... (remaining 15068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19916 2.09 - 4.18: 445 4.18 - 6.28: 47 6.28 - 8.37: 7 8.37 - 10.46: 4 Bond angle restraints: 20419 Sorted by residual: angle pdb=" O4' G G 15 " pdb=" C1' G G 15 " pdb=" N9 G G 15 " ideal model delta sigma weight residual 108.20 116.11 -7.91 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N ARG F 279 " pdb=" CA ARG F 279 " pdb=" C ARG F 279 " ideal model delta sigma weight residual 114.56 108.85 5.71 1.27e+00 6.20e-01 2.02e+01 angle pdb=" C3' G G 15 " pdb=" O3' G G 15 " pdb=" P C G 16 " ideal model delta sigma weight residual 120.20 126.41 -6.21 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CB MET F 468 " pdb=" CG MET F 468 " pdb=" SD MET F 468 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N SER F 440 " pdb=" CA SER F 440 " pdb=" C SER F 440 " ideal model delta sigma weight residual 110.61 114.87 -4.26 1.25e+00 6.40e-01 1.16e+01 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 8813 35.05 - 70.09: 154 70.09 - 105.14: 4 105.14 - 140.19: 2 140.19 - 175.23: 3 Dihedral angle restraints: 8976 sinusoidal: 3919 harmonic: 5057 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -3.18 -156.82 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 43.41 -171.41 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -41.40 -118.60 1 1.50e+01 4.44e-03 6.31e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1826 0.060 - 0.120: 371 0.120 - 0.181: 61 0.181 - 0.241: 7 0.241 - 0.301: 2 Chirality restraints: 2267 Sorted by residual: chirality pdb=" C1' G G 15 " pdb=" O4' G G 15 " pdb=" C2' G G 15 " pdb=" N9 G G 15 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER B 33 " pdb=" N SER B 33 " pdb=" C SER B 33 " pdb=" CB SER B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ARG D 137 " pdb=" N ARG D 137 " pdb=" C ARG D 137 " pdb=" CB ARG D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2264 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 15 " 0.043 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 G G 15 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G G 15 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G G 15 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G G 15 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G G 15 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G G 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G G 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G G 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 135 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 136 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 46 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 47 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " 0.028 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 99 2.54 - 3.13: 11025 3.13 - 3.72: 20974 3.72 - 4.31: 29287 4.31 - 4.90: 49855 Nonbonded interactions: 111240 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.945 3.120 nonbonded pdb=" O ILE A 19 " pdb=" O2' G G 15 " model vdw 1.982 3.040 nonbonded pdb=" OG1 THR B 126 " pdb=" OD1 ASN B 135 " model vdw 2.060 3.040 nonbonded pdb=" OH TYR H 148 " pdb=" O2' A G 7 " model vdw 2.126 3.040 nonbonded pdb=" O SER F 11 " pdb=" ND1 HIS F 14 " model vdw 2.137 3.120 ... (remaining 111235 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 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'B' and (resid 2 through 23 or resid 33 through 120 or resid 141 through \ 214)) selection = (chain 'C' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'D' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'E' and (resid 2 through 63 or resid 76 through 214)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.750 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15074 Z= 0.293 Angle : 0.767 10.461 20421 Z= 0.434 Chirality : 0.050 0.301 2267 Planarity : 0.004 0.054 2531 Dihedral : 13.916 175.232 5723 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1718 helix: 0.56 (0.21), residues: 632 sheet: 0.13 (0.28), residues: 343 loop : -1.98 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 187 TYR 0.021 0.002 TYR C 206 PHE 0.025 0.002 PHE C 166 TRP 0.009 0.001 TRP F 339 HIS 0.018 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (15073) covalent geometry : angle 0.76608 / 0.43 (20419) SS BOND : bond 0.00504 / 0.27 ( 1) SS BOND : angle 3.27684 / 1.78 ( 2) hydrogen bonds : bond 0.13583 / 8.89 ( 623) hydrogen bonds : angle 6.07084 / 4.23 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1555 time to fit residues: 59.6843 Evaluate side-chains 119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN E 40 GLN E 69 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS F 183 GLN F 295 GLN F 493 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.059701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.044555 restraints weight = 78560.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045979 restraints weight = 43208.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046941 restraints weight = 29702.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.047602 restraints weight = 23137.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047867 restraints weight = 19520.755| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15074 Z= 0.166 Angle : 0.654 10.427 20421 Z= 0.353 Chirality : 0.045 0.213 2267 Planarity : 0.004 0.046 2531 Dihedral : 11.781 179.334 2260 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.55 % Allowed : 8.38 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1718 helix: 1.14 (0.20), residues: 647 sheet: 0.51 (0.29), residues: 334 loop : -1.76 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 78 TYR 0.012 0.001 TYR H 255 PHE 0.018 0.001 PHE E 148 TRP 0.022 0.002 TRP H 52 HIS 0.016 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (15073) covalent geometry : angle 0.65346 / 0.35 (20419) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 2.29837 / 1.29 ( 2) hydrogen bonds : bond 0.04491 / 3.06 ( 623) hydrogen bonds : angle 5.02781 / 3.49 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 GLN cc_start: 0.8480 (tt0) cc_final: 0.8269 (tt0) REVERT: E 147 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8054 (mm-30) REVERT: F 8 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.9343 (mtm) REVERT: F 184 TRP cc_start: 0.9038 (t60) cc_final: 0.8776 (t60) REVERT: F 290 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8982 (tp30) REVERT: F 331 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 565 PHE cc_start: 0.9175 (m-80) cc_final: 0.8592 (m-80) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 0.1387 time to fit residues: 31.0060 Evaluate side-chains 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 MET Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 138 GLN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.059173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044279 restraints weight = 78517.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045725 restraints weight = 43056.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046686 restraints weight = 29411.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047296 restraints weight = 22738.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047564 restraints weight = 19267.472| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15074 Z= 0.135 Angle : 0.586 9.395 20421 Z= 0.313 Chirality : 0.043 0.329 2267 Planarity : 0.003 0.040 2531 Dihedral : 11.553 176.911 2260 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.81 % Allowed : 10.12 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1718 helix: 1.44 (0.21), residues: 647 sheet: 0.89 (0.30), residues: 325 loop : -1.66 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 187 TYR 0.022 0.001 TYR A 180 PHE 0.022 0.001 PHE E 148 TRP 0.018 0.001 TRP H 52 HIS 0.015 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15073) covalent geometry : angle 0.58619 / 0.31 (20419) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 1.85608 / 1.05 ( 2) hydrogen bonds : bond 0.03903 / 2.67 ( 623) hydrogen bonds : angle 4.76011 / 3.31 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8159 (mm-30) REVERT: F 1 MET cc_start: 0.7400 (mmt) cc_final: 0.7025 (mmt) REVERT: F 184 TRP cc_start: 0.9004 (t60) cc_final: 0.8760 (t60) REVERT: F 290 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8996 (tp30) REVERT: F 565 PHE cc_start: 0.9183 (m-80) cc_final: 0.8572 (m-80) outliers start: 28 outliers final: 14 residues processed: 128 average time/residue: 0.1290 time to fit residues: 24.3459 Evaluate side-chains 111 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 HIS D 125 ASN H 174 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.055168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040488 restraints weight = 83672.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041824 restraints weight = 46415.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042676 restraints weight = 32174.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043244 restraints weight = 25460.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043655 restraints weight = 21786.986| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15074 Z= 0.299 Angle : 0.722 9.591 20421 Z= 0.384 Chirality : 0.046 0.218 2267 Planarity : 0.004 0.038 2531 Dihedral : 11.665 172.601 2260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.39 % Allowed : 11.54 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1718 helix: 1.05 (0.20), residues: 648 sheet: 0.59 (0.29), residues: 330 loop : -1.75 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 37 TYR 0.028 0.002 TYR A 180 PHE 0.025 0.002 PHE E 148 TRP 0.014 0.002 TRP H 52 HIS 0.010 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 (15073) covalent geometry : angle 0.72154 / 0.38 (20419) SS BOND : bond 0.00644 / 0.34 ( 1) SS BOND : angle 1.73774 / 0.96 ( 2) hydrogen bonds : bond 0.04821 / 3.38 ( 623) hydrogen bonds : angle 4.98378 / 3.50 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASP cc_start: 0.8548 (t0) cc_final: 0.8297 (t0) REVERT: A 180 TYR cc_start: 0.9093 (p90) cc_final: 0.8759 (p90) REVERT: B 193 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 67 MET cc_start: 0.8239 (tmm) cc_final: 0.7641 (tmm) REVERT: E 78 ARG cc_start: 0.8895 (mtt90) cc_final: 0.8638 (mtm-85) REVERT: E 147 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8258 (mt-10) REVERT: H 13 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8054 (pttt) REVERT: H 50 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9305 (t) REVERT: F 1 MET cc_start: 0.7996 (mmt) cc_final: 0.7510 (mmt) REVERT: F 257 MET cc_start: 0.8230 (mpp) cc_final: 0.8002 (mpp) REVERT: F 290 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9012 (tp30) outliers start: 37 outliers final: 21 residues processed: 122 average time/residue: 0.1277 time to fit residues: 23.0891 Evaluate side-chains 102 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 169 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 104 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN E 72 HIS H 129 GLN H 214 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.057380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042585 restraints weight = 81019.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044020 restraints weight = 44090.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044932 restraints weight = 30235.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.045567 restraints weight = 23653.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.045980 restraints weight = 19977.247| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15074 Z= 0.113 Angle : 0.564 12.081 20421 Z= 0.303 Chirality : 0.042 0.187 2267 Planarity : 0.003 0.035 2531 Dihedral : 11.298 178.151 2260 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.81 % Allowed : 13.28 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1718 helix: 1.60 (0.21), residues: 647 sheet: 0.82 (0.29), residues: 324 loop : -1.61 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 37 TYR 0.014 0.001 TYR A 180 PHE 0.024 0.001 PHE E 148 TRP 0.025 0.002 TRP F 184 HIS 0.012 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15073) covalent geometry : angle 0.56355 / 0.30 (20419) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 1.46737 / 0.82 ( 2) hydrogen bonds : bond 0.03663 / 2.50 ( 623) hydrogen bonds : angle 4.62477 / 3.23 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9182 (m) cc_final: 0.8975 (p) REVERT: A 179 ASP cc_start: 0.7913 (t0) cc_final: 0.7639 (t0) REVERT: B 88 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7830 (tttt) REVERT: D 67 MET cc_start: 0.7622 (pmm) cc_final: 0.6873 (pmm) REVERT: E 147 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8179 (mt-10) REVERT: H 13 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7709 (pttt) REVERT: F 1 MET cc_start: 0.8019 (mmt) cc_final: 0.7618 (mmt) REVERT: F 252 PHE cc_start: 0.8817 (p90) cc_final: 0.8578 (p90) REVERT: F 257 MET cc_start: 0.8242 (mpp) cc_final: 0.7788 (mpp) REVERT: F 290 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9023 (tp30) outliers start: 28 outliers final: 17 residues processed: 112 average time/residue: 0.1094 time to fit residues: 18.3643 Evaluate side-chains 101 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 165 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.054901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040321 restraints weight = 83581.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041676 restraints weight = 46286.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042549 restraints weight = 31983.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043138 restraints weight = 25102.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043523 restraints weight = 21369.919| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15074 Z= 0.261 Angle : 0.654 10.813 20421 Z= 0.347 Chirality : 0.044 0.188 2267 Planarity : 0.004 0.043 2531 Dihedral : 11.345 173.507 2260 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.13 % Allowed : 14.12 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1718 helix: 1.34 (0.20), residues: 648 sheet: 0.62 (0.28), residues: 337 loop : -1.66 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 37 TYR 0.016 0.002 TYR A 180 PHE 0.014 0.002 PHE E 148 TRP 0.033 0.003 TRP F 184 HIS 0.011 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (15073) covalent geometry : angle 0.65403 / 0.35 (20419) SS BOND : bond 0.00548 / 0.29 ( 1) SS BOND : angle 1.57687 / 0.87 ( 2) hydrogen bonds : bond 0.04367 / 3.02 ( 623) hydrogen bonds : angle 4.84876 / 3.41 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 MET cc_start: 0.8296 (tmm) cc_final: 0.7673 (tmm) REVERT: E 37 ARG cc_start: 0.9121 (mtt90) cc_final: 0.8669 (mpt-90) REVERT: E 147 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8269 (mt-10) REVERT: H 13 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7908 (pttt) REVERT: H 50 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9275 (t) REVERT: F 8 MET cc_start: 0.9496 (mtm) cc_final: 0.8643 (mtm) REVERT: F 264 ASP cc_start: 0.8876 (t0) cc_final: 0.8650 (t0) REVERT: F 290 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9084 (tp30) REVERT: F 452 MET cc_start: 0.8291 (tpp) cc_final: 0.7920 (mmm) outliers start: 33 outliers final: 21 residues processed: 104 average time/residue: 0.1150 time to fit residues: 18.5022 Evaluate side-chains 95 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.056124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041565 restraints weight = 82058.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042942 restraints weight = 44541.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043849 restraints weight = 30569.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044449 restraints weight = 23883.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044820 restraints weight = 20278.607| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15074 Z= 0.139 Angle : 0.564 10.407 20421 Z= 0.299 Chirality : 0.042 0.171 2267 Planarity : 0.003 0.036 2531 Dihedral : 11.197 176.873 2260 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.81 % Allowed : 14.64 % 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: 0.20 (0.20), residues: 1718 helix: 1.66 (0.21), residues: 647 sheet: 0.78 (0.29), residues: 323 loop : -1.62 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 37 TYR 0.011 0.001 TYR A 180 PHE 0.022 0.001 PHE E 152 TRP 0.022 0.002 TRP F 184 HIS 0.018 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (15073) covalent geometry : angle 0.56390 / 0.30 (20419) SS BOND : bond 0.00348 / 0.18 ( 1) SS BOND : angle 1.47192 / 0.83 ( 2) hydrogen bonds : bond 0.03724 / 2.54 ( 623) hydrogen bonds : angle 4.61358 / 3.22 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 ARG cc_start: 0.9048 (mtt90) cc_final: 0.8832 (mtm-85) REVERT: E 147 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8182 (mt-10) REVERT: H 13 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7759 (pttt) REVERT: F 41 LEU cc_start: 0.8909 (tt) cc_final: 0.8549 (mt) REVERT: F 252 PHE cc_start: 0.8899 (p90) cc_final: 0.8633 (p90) REVERT: F 264 ASP cc_start: 0.8861 (t0) cc_final: 0.8652 (t0) REVERT: F 290 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9127 (tp30) REVERT: F 452 MET cc_start: 0.8364 (tpp) cc_final: 0.8096 (mmm) outliers start: 28 outliers final: 21 residues processed: 104 average time/residue: 0.1061 time to fit residues: 16.8714 Evaluate side-chains 99 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.0060 chunk 138 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.056765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042183 restraints weight = 81258.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043562 restraints weight = 44356.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.044484 restraints weight = 30441.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045050 restraints weight = 23763.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045309 restraints weight = 20279.202| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15074 Z= 0.115 Angle : 0.570 14.134 20421 Z= 0.296 Chirality : 0.041 0.173 2267 Planarity : 0.003 0.040 2531 Dihedral : 11.095 177.246 2260 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.55 % Allowed : 15.28 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1718 helix: 1.77 (0.21), residues: 648 sheet: 0.86 (0.28), residues: 323 loop : -1.60 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 37 TYR 0.014 0.001 TYR F 463 PHE 0.024 0.001 PHE E 152 TRP 0.031 0.003 TRP F 184 HIS 0.016 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15073) covalent geometry : angle 0.56987 / 0.30 (20419) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 1.31042 / 0.74 ( 2) hydrogen bonds : bond 0.03462 / 2.35 ( 623) hydrogen bonds : angle 4.52933 / 3.16 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8204 (mt-10) REVERT: H 13 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7632 (pttt) REVERT: F 1 MET cc_start: 0.8059 (mmt) cc_final: 0.7690 (mmt) REVERT: F 41 LEU cc_start: 0.8930 (tt) cc_final: 0.8657 (tp) REVERT: F 252 PHE cc_start: 0.8810 (p90) cc_final: 0.8520 (p90) REVERT: F 264 ASP cc_start: 0.8872 (t0) cc_final: 0.8667 (t0) REVERT: F 290 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9059 (tp30) outliers start: 24 outliers final: 19 residues processed: 103 average time/residue: 0.1235 time to fit residues: 19.1623 Evaluate side-chains 99 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 175 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.056736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042219 restraints weight = 82379.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043586 restraints weight = 44559.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044483 restraints weight = 30556.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045094 restraints weight = 23963.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045476 restraints weight = 20272.531| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15074 Z= 0.124 Angle : 0.602 19.354 20421 Z= 0.306 Chirality : 0.041 0.197 2267 Planarity : 0.003 0.079 2531 Dihedral : 11.065 176.739 2260 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 15.22 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1718 helix: 1.82 (0.21), residues: 648 sheet: 0.87 (0.28), residues: 323 loop : -1.56 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 144 TYR 0.011 0.001 TYR F 463 PHE 0.031 0.001 PHE E 152 TRP 0.035 0.003 TRP F 184 HIS 0.015 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15073) covalent geometry : angle 0.60151 / 0.31 (20419) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 1.25141 / 0.70 ( 2) hydrogen bonds : bond 0.03487 / 2.36 ( 623) hydrogen bonds : angle 4.50326 / 3.14 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8134 (mt-10) REVERT: H 13 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7567 (pttt) REVERT: F 1 MET cc_start: 0.8093 (mmt) cc_final: 0.7741 (mmt) REVERT: F 8 MET cc_start: 0.9494 (mtm) cc_final: 0.8822 (mtm) REVERT: F 41 LEU cc_start: 0.8884 (tt) cc_final: 0.8678 (tp) REVERT: F 252 PHE cc_start: 0.8809 (p90) cc_final: 0.8512 (p90) REVERT: F 264 ASP cc_start: 0.8866 (t0) cc_final: 0.8656 (t0) REVERT: F 290 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9035 (tp30) outliers start: 24 outliers final: 22 residues processed: 105 average time/residue: 0.1252 time to fit residues: 19.9108 Evaluate side-chains 101 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041110 restraints weight = 83086.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042453 restraints weight = 45394.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043349 restraints weight = 31266.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.043953 restraints weight = 24447.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044328 restraints weight = 20732.113| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15074 Z= 0.182 Angle : 0.640 13.168 20421 Z= 0.329 Chirality : 0.042 0.194 2267 Planarity : 0.003 0.035 2531 Dihedral : 11.132 175.091 2260 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.87 % Allowed : 15.09 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1718 helix: 1.74 (0.21), residues: 648 sheet: 0.73 (0.28), residues: 326 loop : -1.59 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 144 TYR 0.058 0.001 TYR F 284 PHE 0.031 0.001 PHE E 152 TRP 0.036 0.003 TRP F 184 HIS 0.016 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15073) covalent geometry : angle 0.63991 / 0.33 (20419) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 1.31484 / 0.73 ( 2) hydrogen bonds : bond 0.03859 / 2.64 ( 623) hydrogen bonds : angle 4.61362 / 3.23 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8092 (mpt180) REVERT: E 147 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8228 (mt-10) REVERT: H 13 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7673 (pttt) REVERT: H 50 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9253 (t) REVERT: F 8 MET cc_start: 0.9508 (mtm) cc_final: 0.8807 (mtm) REVERT: F 41 LEU cc_start: 0.8871 (tt) cc_final: 0.8546 (mt) REVERT: F 252 PHE cc_start: 0.8960 (p90) cc_final: 0.8687 (p90) REVERT: F 264 ASP cc_start: 0.8852 (t0) cc_final: 0.8650 (t0) REVERT: F 290 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9032 (tp30) outliers start: 29 outliers final: 23 residues processed: 104 average time/residue: 0.1298 time to fit residues: 20.3932 Evaluate side-chains 103 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039386 restraints weight = 84878.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040711 restraints weight = 46488.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041581 restraints weight = 31947.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042125 restraints weight = 25046.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042533 restraints weight = 21387.448| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15074 Z= 0.304 Angle : 0.737 13.753 20421 Z= 0.385 Chirality : 0.045 0.197 2267 Planarity : 0.004 0.035 2531 Dihedral : 11.382 172.977 2260 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.74 % Allowed : 15.60 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1718 helix: 1.20 (0.20), residues: 649 sheet: 0.60 (0.29), residues: 317 loop : -1.69 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 144 TYR 0.021 0.002 TYR F 284 PHE 0.031 0.002 PHE E 152 TRP 0.040 0.003 TRP F 184 HIS 0.018 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.30 (15073) covalent geometry : angle 0.73663 / 0.38 (20419) SS BOND : bond 0.00714 / 0.38 ( 1) SS BOND : angle 1.65658 / 0.91 ( 2) hydrogen bonds : bond 0.04580 / 3.18 ( 623) hydrogen bonds : angle 4.94315 / 3.47 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.88 seconds wall clock time: 46 minutes 31.35 seconds (2791.35 seconds total)