Starting phenix.real_space_refine on Sat Sep 12 09:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzw_26920/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzw_26920/09_2026/7uzw_26920.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 3.27, per 1000 atoms: 0.22 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: 1.26 Conformation dependent library (CDL) restraints added in 630.4 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: 1.91 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: 2.69 Time building geometry restraints manager: 1.68 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 1.478 1.563 -0.085 2.00e-02 2.50e+03 1.80e+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: 19816 2.09 - 4.18: 518 4.18 - 6.28: 72 6.28 - 8.37: 9 8.37 - 10.46: 4 Bond angle restraints: 20419 Sorted by residual: angle pdb=" C3' G G 15 " pdb=" O3' G G 15 " pdb=" P C G 16 " ideal model delta sigma weight residual 119.70 126.41 -6.71 1.20e+00 6.94e-01 3.13e+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=" O4' G G 15 " pdb=" C1' G G 15 " pdb=" N9 G G 15 " ideal model delta sigma weight residual 108.50 116.11 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" O3' A G 27 " pdb=" C3' A G 27 " pdb=" C2' A G 27 " ideal model delta sigma weight residual 113.80 106.82 6.98 2.00e+00 2.50e-01 1.22e+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 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 8762 35.05 - 70.09: 201 70.09 - 105.14: 12 105.14 - 140.19: 0 140.19 - 175.23: 1 Dihedral angle restraints: 8976 sinusoidal: 3919 harmonic: 5057 Sorted by residual: dihedral pdb=" C4' A G 27 " pdb=" C3' A G 27 " pdb=" C2' A G 27 " pdb=" C1' A G 27 " ideal model delta sinusoidal sigma weight residual 36.34 -40.95 77.29 1 3.10e+00 1.04e-01 7.79e+02 dihedral pdb=" C4' G G 3 " pdb=" C3' G G 3 " pdb=" C2' G G 3 " pdb=" C1' G G 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.30 74.64 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' A G 1 " pdb=" C3' A G 1 " pdb=" C2' A G 1 " pdb=" C1' A G 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.56 73.91 1 3.10e+00 1.04e-01 7.22e+02 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1975 0.080 - 0.160: 229 0.160 - 0.240: 42 0.240 - 0.320: 19 0.320 - 0.399: 2 Chirality restraints: 2267 Sorted by residual: chirality pdb=" P C G 16 " pdb=" OP1 C G 16 " pdb=" OP2 C G 16 " pdb=" O5' C G 16 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C3' A G 27 " pdb=" C4' A G 27 " pdb=" O3' A G 27 " pdb=" C2' A G 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.33 2.00e-01 2.50e+01 2.66e+00 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 2.46 2.14 0.32 2.00e-01 2.50e+01 2.55e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- 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 0.085 15074 Z= 0.292 Angle : 0.810 10.461 20421 Z= 0.442 Chirality : 0.062 0.399 2267 Planarity : 0.004 0.054 2531 Dihedral : 14.664 175.232 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 0.00638 / 0.29 (15073) covalent geometry : angle 0.80939 / 0.44 (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 : 0.616 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: 0.1549 time to fit residues: 59.3957 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 : 0.606 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.060131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045079 restraints weight = 79225.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046521 restraints weight = 43340.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047503 restraints weight = 29624.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048171 restraints weight = 23029.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048598 restraints weight = 19397.257| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15074 Z= 0.181 Angle : 0.909 21.633 20421 Z= 0.426 Chirality : 0.073 1.199 2267 Planarity : 0.004 0.050 2531 Dihedral : 10.640 173.259 2260 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.61 % Allowed : 8.38 % Favored : 90.01 % 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: -0.28 (0.20), residues: 1718 helix: 1.13 (0.20), residues: 647 sheet: 0.49 (0.29), residues: 334 loop : -1.77 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.013 0.001 TYR H 255 PHE 0.018 0.001 PHE E 148 TRP 0.023 0.002 TRP H 52 HIS 0.017 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (15073) covalent geometry : angle 0.90841 / 0.43 (20419) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 2.30663 / 1.29 ( 2) hydrogen bonds : bond 0.04517 / 3.07 ( 623) hydrogen bonds : angle 5.08313 / 3.52 ( 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: 25 poor density : 136 time to evaluate : 0.591 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: B 193 GLN cc_start: 0.8392 (tt0) cc_final: 0.8185 (tt0) REVERT: E 147 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8011 (mm-30) REVERT: F 8 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.9363 (mtm) REVERT: F 184 TRP cc_start: 0.9039 (t60) cc_final: 0.8780 (t60) REVERT: F 290 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8978 (tp30) REVERT: F 300 LEU cc_start: 0.9281 (mt) cc_final: 0.8970 (pp) REVERT: F 331 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 565 PHE cc_start: 0.9173 (m-80) cc_final: 0.8574 (m-80) outliers start: 25 outliers final: 16 residues processed: 154 average time/residue: 0.1353 time to fit residues: 30.4381 Evaluate side-chains 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 193 GLN 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: 4.9990 chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 170 optimal weight: 0.0470 chunk 112 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 GLN D 138 GLN E 69 GLN E 74 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.059505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044488 restraints weight = 79920.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045942 restraints weight = 43713.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046928 restraints weight = 29791.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047564 restraints weight = 23038.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047981 restraints weight = 19417.192| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15074 Z= 0.149 Angle : 0.747 11.919 20421 Z= 0.357 Chirality : 0.061 0.750 2267 Planarity : 0.003 0.037 2531 Dihedral : 10.619 161.463 2260 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.87 % Allowed : 10.32 % Favored : 87.81 % 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: 0.05 (0.20), residues: 1718 helix: 1.40 (0.20), residues: 648 sheet: 0.88 (0.30), residues: 325 loop : -1.67 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 187 TYR 0.020 0.001 TYR A 180 PHE 0.020 0.001 PHE E 148 TRP 0.017 0.001 TRP H 52 HIS 0.016 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15073) covalent geometry : angle 0.74701 / 0.36 (20419) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 1.89191 / 1.07 ( 2) hydrogen bonds : bond 0.03958 / 2.71 ( 623) hydrogen bonds : angle 4.79285 / 3.33 ( 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 139 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.590 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: A 180 TYR cc_start: 0.8607 (p90) cc_final: 0.8200 (p90) REVERT: B 88 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7986 (tttt) REVERT: E 103 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: E 147 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8137 (mm-30) REVERT: E 193 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7693 (tp40) REVERT: F 1 MET cc_start: 0.7434 (mmt) cc_final: 0.7061 (mmt) REVERT: F 184 TRP cc_start: 0.9021 (t60) cc_final: 0.8777 (t60) REVERT: F 290 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9003 (tp30) REVERT: F 300 LEU cc_start: 0.9310 (mt) cc_final: 0.9006 (tt) REVERT: F 565 PHE cc_start: 0.9201 (m-80) cc_final: 0.8586 (m-80) outliers start: 29 outliers final: 14 residues processed: 134 average time/residue: 0.1383 time to fit residues: 27.1624 Evaluate side-chains 112 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 35 LEU 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 192 VAL 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: 6.9990 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.058071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043351 restraints weight = 81092.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044760 restraints weight = 44311.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045685 restraints weight = 30292.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046310 restraints weight = 23646.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046680 restraints weight = 19979.843| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15074 Z= 0.187 Angle : 0.733 12.452 20421 Z= 0.353 Chirality : 0.058 0.628 2267 Planarity : 0.003 0.046 2531 Dihedral : 10.886 162.686 2260 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.32 % Allowed : 10.96 % Favored : 86.72 % 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: 0.12 (0.20), residues: 1718 helix: 1.53 (0.20), residues: 648 sheet: 0.79 (0.29), residues: 338 loop : -1.68 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 37 TYR 0.016 0.001 TYR A 180 PHE 0.024 0.001 PHE E 148 TRP 0.010 0.001 TRP H 52 HIS 0.007 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (15073) covalent geometry : angle 0.73308 / 0.35 (20419) SS BOND : bond 0.00418 / 0.22 ( 1) SS BOND : angle 1.55573 / 0.87 ( 2) hydrogen bonds : bond 0.03950 / 2.72 ( 623) hydrogen bonds : angle 4.70732 / 3.28 ( 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 131 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.623 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 179 ASP cc_start: 0.7918 (t0) cc_final: 0.7706 (t0) REVERT: E 37 ARG cc_start: 0.9121 (mtt90) cc_final: 0.8849 (mtt90) REVERT: H 13 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7732 (pttt) REVERT: F 1 MET cc_start: 0.7903 (mmt) cc_final: 0.7495 (mmt) REVERT: F 257 MET cc_start: 0.8220 (mpp) cc_final: 0.7706 (mpp) REVERT: F 290 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8954 (tp30) REVERT: F 300 LEU cc_start: 0.9316 (mt) cc_final: 0.9049 (tt) outliers start: 36 outliers final: 21 residues processed: 124 average time/residue: 0.1164 time to fit residues: 22.2041 Evaluate side-chains 103 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 193 GLN 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 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 78 THR 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: 4.9990 chunk 76 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS D 125 ASN H 129 GLN H 214 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.058043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043315 restraints weight = 80996.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044743 restraints weight = 44253.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045662 restraints weight = 30177.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046300 restraints weight = 23494.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.046682 restraints weight = 19855.849| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15074 Z= 0.153 Angle : 0.705 13.440 20421 Z= 0.337 Chirality : 0.056 0.542 2267 Planarity : 0.003 0.034 2531 Dihedral : 11.049 177.706 2260 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.06 % Allowed : 12.96 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1718 helix: 1.63 (0.21), residues: 648 sheet: 0.96 (0.29), residues: 324 loop : -1.60 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 37 TYR 0.019 0.001 TYR H 255 PHE 0.017 0.001 PHE H 121 TRP 0.030 0.002 TRP F 184 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15073) covalent geometry : angle 0.70470 / 0.34 (20419) SS BOND : bond 0.00354 / 0.19 ( 1) SS BOND : angle 1.43956 / 0.80 ( 2) hydrogen bonds : bond 0.03728 / 2.56 ( 623) hydrogen bonds : angle 4.64882 / 3.24 ( 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 121 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.598 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: A 91 ILE cc_start: 0.8722 (mm) cc_final: 0.8514 (mm) REVERT: B 88 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7788 (tttt) REVERT: D 67 MET cc_start: 0.7637 (pmm) cc_final: 0.7424 (pmm) REVERT: E 147 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8094 (mt-10) REVERT: H 13 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7703 (pttt) REVERT: F 1 MET cc_start: 0.8020 (mmt) cc_final: 0.7581 (mmt) REVERT: F 160 MET cc_start: 0.7058 (ptm) cc_final: 0.6842 (ptm) REVERT: F 264 ASP cc_start: 0.8873 (t0) cc_final: 0.8649 (t0) REVERT: F 290 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8965 (tp30) REVERT: F 300 LEU cc_start: 0.9276 (mt) cc_final: 0.9068 (tt) outliers start: 32 outliers final: 25 residues processed: 114 average time/residue: 0.1224 time to fit residues: 21.4933 Evaluate side-chains 110 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 151 VAL 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 193 GLN 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 F residue 2 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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: 7.9990 chunk 163 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 0.0270 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 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 = 0.3509 r_free = 0.3509 target = 0.058979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044204 restraints weight = 80530.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045670 restraints weight = 44342.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.046635 restraints weight = 30326.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047273 restraints weight = 23512.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047677 restraints weight = 19873.301| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15074 Z= 0.111 Angle : 0.658 12.951 20421 Z= 0.312 Chirality : 0.054 0.449 2267 Planarity : 0.003 0.042 2531 Dihedral : 10.912 170.052 2260 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.06 % Allowed : 13.22 % Favored : 84.72 % 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: 0.44 (0.20), residues: 1718 helix: 1.84 (0.21), residues: 647 sheet: 1.08 (0.29), residues: 323 loop : -1.55 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 37 TYR 0.021 0.001 TYR H 255 PHE 0.022 0.001 PHE E 152 TRP 0.031 0.002 TRP F 184 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15073) covalent geometry : angle 0.65753 / 0.31 (20419) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 1.22611 / 0.69 ( 2) hydrogen bonds : bond 0.03290 / 2.22 ( 623) hydrogen bonds : angle 4.47724 / 3.11 ( 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 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.612 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: B 131 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8777 (p) REVERT: D 67 MET cc_start: 0.7753 (pmm) cc_final: 0.7530 (pmm) REVERT: E 147 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8039 (mt-10) REVERT: H 13 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7438 (pttt) REVERT: F 1 MET cc_start: 0.8021 (mmt) cc_final: 0.7664 (mmt) REVERT: F 8 MET cc_start: 0.9551 (mtm) cc_final: 0.8726 (mtm) REVERT: F 264 ASP cc_start: 0.8861 (t0) cc_final: 0.8634 (t0) REVERT: F 286 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9082 (mm-30) REVERT: F 290 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9024 (tp30) outliers start: 32 outliers final: 24 residues processed: 116 average time/residue: 0.1190 time to fit residues: 21.4758 Evaluate side-chains 109 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 151 VAL 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 201 THR 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 52 TRP Chi-restraints excluded: chain H residue 62 THR 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 203 ASP Chi-restraints excluded: chain F residue 286 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 72 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 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 = 0.3432 r_free = 0.3432 target = 0.056091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041499 restraints weight = 82545.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042878 restraints weight = 45749.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043778 restraints weight = 31537.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044393 restraints weight = 24655.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044800 restraints weight = 20864.316| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15074 Z= 0.229 Angle : 0.762 14.284 20421 Z= 0.365 Chirality : 0.058 0.581 2267 Planarity : 0.003 0.027 2531 Dihedral : 11.195 168.806 2260 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.06 % Allowed : 13.99 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1718 helix: 1.53 (0.20), residues: 648 sheet: 0.79 (0.28), residues: 337 loop : -1.59 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.016 0.001 TYR A 180 PHE 0.017 0.002 PHE E 152 TRP 0.029 0.002 TRP F 184 HIS 0.007 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (15073) covalent geometry : angle 0.76237 / 0.36 (20419) SS BOND : bond 0.00442 / 0.23 ( 1) SS BOND : angle 1.49074 / 0.83 ( 2) hydrogen bonds : bond 0.04238 / 2.95 ( 623) hydrogen bonds : angle 4.72582 / 3.30 ( 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 114 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.594 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: 0.8388 (mt-10) cc_final: 0.8150 (mt-10) REVERT: H 13 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7607 (pttt) REVERT: F 1 MET cc_start: 0.8195 (mmt) cc_final: 0.7841 (mmt) REVERT: F 8 MET cc_start: 0.9511 (mtm) cc_final: 0.8688 (mtm) REVERT: F 264 ASP cc_start: 0.8858 (t0) cc_final: 0.8618 (t0) REVERT: F 290 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9007 (tp30) outliers start: 32 outliers final: 23 residues processed: 110 average time/residue: 0.1133 time to fit residues: 19.2385 Evaluate side-chains 96 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE 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 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 F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 163 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.057338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042753 restraints weight = 80821.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044175 restraints weight = 44386.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045112 restraints weight = 30410.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045733 restraints weight = 23599.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046119 restraints weight = 19938.133| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15074 Z= 0.130 Angle : 0.693 13.448 20421 Z= 0.329 Chirality : 0.054 0.455 2267 Planarity : 0.003 0.028 2531 Dihedral : 11.067 170.477 2260 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.74 % Allowed : 14.96 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1718 helix: 1.75 (0.21), residues: 647 sheet: 0.97 (0.29), residues: 323 loop : -1.59 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 37 TYR 0.013 0.001 TYR F 463 PHE 0.024 0.001 PHE E 152 TRP 0.029 0.002 TRP F 184 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15073) covalent geometry : angle 0.69260 / 0.33 (20419) SS BOND : bond 0.00242 / 0.13 ( 1) SS BOND : angle 1.33251 / 0.75 ( 2) hydrogen bonds : bond 0.03566 / 2.44 ( 623) hydrogen bonds : angle 4.56597 / 3.17 ( 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 108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8455 (pttm) REVERT: E 147 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8124 (mt-10) REVERT: H 13 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7497 (pttt) REVERT: F 1 MET cc_start: 0.8090 (mmt) cc_final: 0.7746 (mmt) REVERT: F 8 MET cc_start: 0.9556 (mtm) cc_final: 0.8737 (mtm) REVERT: F 41 LEU cc_start: 0.8791 (tt) cc_final: 0.8417 (mt) REVERT: F 264 ASP cc_start: 0.8822 (t0) cc_final: 0.8604 (t0) REVERT: F 290 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9012 (tp30) outliers start: 27 outliers final: 21 residues processed: 104 average time/residue: 0.1157 time to fit residues: 18.5695 Evaluate side-chains 99 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 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 126 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE 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 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 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 203 ASP 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: 4.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 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 = 0.3453 r_free = 0.3453 target = 0.056895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042335 restraints weight = 82586.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043754 restraints weight = 45239.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044696 restraints weight = 30973.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045316 restraints weight = 24011.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.045573 restraints weight = 20275.023| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15074 Z= 0.162 Angle : 0.717 13.878 20421 Z= 0.343 Chirality : 0.055 0.462 2267 Planarity : 0.003 0.077 2531 Dihedral : 11.171 171.088 2260 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.93 % Allowed : 15.02 % 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: 1.65 (0.20), residues: 650 sheet: 0.92 (0.29), residues: 323 loop : -1.61 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 144 TYR 0.012 0.001 TYR A 180 PHE 0.029 0.001 PHE E 152 TRP 0.031 0.003 TRP F 184 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (15073) covalent geometry : angle 0.71665 / 0.34 (20419) SS BOND : bond 0.00377 / 0.20 ( 1) SS BOND : angle 1.28238 / 0.72 ( 2) hydrogen bonds : bond 0.03677 / 2.51 ( 623) hydrogen bonds : angle 4.62264 / 3.22 ( 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 107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8118 (mt-10) REVERT: H 13 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7510 (pttt) REVERT: H 50 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9217 (t) REVERT: F 1 MET cc_start: 0.8097 (mmt) cc_final: 0.7775 (mmt) REVERT: F 41 LEU cc_start: 0.8799 (tt) cc_final: 0.8408 (mt) REVERT: F 264 ASP cc_start: 0.8843 (t0) cc_final: 0.8629 (t0) REVERT: F 284 TYR cc_start: 0.8812 (t80) cc_final: 0.8568 (t80) REVERT: F 288 MET cc_start: 0.9122 (ptp) cc_final: 0.8922 (pmm) REVERT: F 290 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9003 (tp30) outliers start: 30 outliers final: 24 residues processed: 104 average time/residue: 0.1070 time to fit residues: 17.7504 Evaluate side-chains 101 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE 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 F residue 2 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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: 0.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 1 optimal weight: 0.0040 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.0270 overall best weight: 1.0056 ------------------------------------------------------------------------------- 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** E 72 HIS ** 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 = 0.3460 r_free = 0.3460 target = 0.057097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042632 restraints weight = 81876.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.043997 restraints weight = 45436.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044897 restraints weight = 30979.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045571 restraints weight = 24112.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045984 restraints weight = 20271.365| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15074 Z= 0.143 Angle : 0.700 13.846 20421 Z= 0.335 Chirality : 0.054 0.466 2267 Planarity : 0.003 0.028 2531 Dihedral : 11.320 174.028 2260 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.74 % Allowed : 15.28 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1718 helix: 1.73 (0.21), residues: 649 sheet: 0.94 (0.28), residues: 323 loop : -1.60 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 144 TYR 0.011 0.001 TYR F 284 PHE 0.029 0.001 PHE E 152 TRP 0.032 0.003 TRP F 184 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (15073) covalent geometry : angle 0.70018 / 0.34 (20419) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 1.27715 / 0.72 ( 2) hydrogen bonds : bond 0.03519 / 2.39 ( 623) hydrogen bonds : angle 4.57567 / 3.18 ( 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 106 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8117 (mt-10) REVERT: H 13 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7461 (pttt) REVERT: F 41 LEU cc_start: 0.8806 (tt) cc_final: 0.8432 (mt) REVERT: F 264 ASP cc_start: 0.8855 (t0) cc_final: 0.8641 (t0) REVERT: F 288 MET cc_start: 0.9077 (ptp) cc_final: 0.8799 (ptp) REVERT: F 290 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9011 (tp30) outliers start: 27 outliers final: 25 residues processed: 102 average time/residue: 0.1222 time to fit residues: 19.3088 Evaluate side-chains 101 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE 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 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 7 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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: 5.9990 chunk 77 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.056427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042006 restraints weight = 81957.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043346 restraints weight = 45820.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044265 restraints weight = 31122.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044890 restraints weight = 24148.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045302 restraints weight = 20343.056| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15074 Z= 0.172 Angle : 0.710 14.230 20421 Z= 0.341 Chirality : 0.054 0.471 2267 Planarity : 0.003 0.028 2531 Dihedral : 11.382 170.247 2260 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.81 % Allowed : 15.28 % Favored : 82.91 % 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: 0.24 (0.20), residues: 1718 helix: 1.66 (0.20), residues: 649 sheet: 0.85 (0.29), residues: 326 loop : -1.60 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 144 TYR 0.013 0.001 TYR A 180 PHE 0.029 0.001 PHE E 152 TRP 0.031 0.003 TRP F 184 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (15073) covalent geometry : angle 0.71017 / 0.34 (20419) SS BOND : bond 0.00378 / 0.20 ( 1) SS BOND : angle 1.35033 / 0.76 ( 2) hydrogen bonds : bond 0.03707 / 2.53 ( 623) hydrogen bonds : angle 4.61758 / 3.22 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.17 seconds wall clock time: 48 minutes 21.46 seconds (2901.46 seconds total)