Starting phenix.real_space_refine on Fri Jun 13 11:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzw_26920/06_2025/7uzw_26920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzw_26920/06_2025/7uzw_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_26920/06_2025/7uzw_26920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzw_26920/06_2025/7uzw_26920.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzw_26920/06_2025/7uzw_26920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzw_26920/06_2025/7uzw_26920.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1458 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain breaks: 2 Chain: "H" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2355 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3886 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 5, 'TRANS': 472} Chain breaks: 6 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 11, 'rna3p': 19} Time building chain proxies: 10.47, per 1000 atoms: 0.71 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: 3.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.50 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: 4.50 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4805 1.34 - 1.47: 3719 1.47 - 1.60: 6459 1.60 - 1.73: 33 1.73 - 1.85: 57 Bond restraints: 15073 Sorted by residual: bond pdb=" C1' U G 24 " pdb=" N1 U G 24 " ideal model delta sigma weight residual 1.480 1.563 -0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.41e-02 5.03e+03 5.99e+00 bond pdb=" N ARG D 137 " pdb=" CA ARG D 137 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" CB CYS F 214 " pdb=" SG CYS F 214 " ideal model delta sigma weight residual 1.808 1.738 0.070 3.30e-02 9.18e+02 4.54e+00 ... (remaining 15068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19916 2.09 - 4.18: 445 4.18 - 6.28: 47 6.28 - 8.37: 7 8.37 - 10.46: 4 Bond angle restraints: 20419 Sorted by residual: angle pdb=" O4' G G 15 " pdb=" C1' G G 15 " pdb=" N9 G G 15 " ideal model delta sigma weight residual 108.20 116.11 -7.91 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N ARG F 279 " pdb=" CA ARG F 279 " pdb=" C ARG F 279 " ideal model delta sigma weight residual 114.56 108.85 5.71 1.27e+00 6.20e-01 2.02e+01 angle pdb=" C3' G G 15 " pdb=" O3' G G 15 " pdb=" P C G 16 " ideal model delta sigma weight residual 120.20 126.41 -6.21 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CB MET F 468 " pdb=" CG MET F 468 " pdb=" SD MET F 468 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N SER F 440 " pdb=" CA SER F 440 " pdb=" C SER F 440 " ideal model delta sigma weight residual 110.61 114.87 -4.26 1.25e+00 6.40e-01 1.16e+01 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 8853 35.05 - 70.09: 192 70.09 - 105.14: 10 105.14 - 140.19: 2 140.19 - 175.23: 3 Dihedral angle restraints: 9060 sinusoidal: 4003 harmonic: 5057 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -3.18 -156.82 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 43.41 -171.41 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -41.40 -118.60 1 1.50e+01 4.44e-03 6.31e+01 ... (remaining 9057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1826 0.060 - 0.120: 371 0.120 - 0.181: 61 0.181 - 0.241: 7 0.241 - 0.301: 2 Chirality restraints: 2267 Sorted by residual: chirality pdb=" C1' G G 15 " pdb=" O4' G G 15 " pdb=" C2' G G 15 " pdb=" N9 G G 15 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER B 33 " pdb=" N SER B 33 " pdb=" C SER B 33 " pdb=" CB SER B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ARG D 137 " pdb=" N ARG D 137 " pdb=" C ARG D 137 " pdb=" CB ARG D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2264 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 15 " 0.043 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 G G 15 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G G 15 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G G 15 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G G 15 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G G 15 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G G 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G G 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G G 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 135 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 136 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 46 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 47 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " 0.028 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 99 2.54 - 3.13: 11025 3.13 - 3.72: 20974 3.72 - 4.31: 29287 4.31 - 4.90: 49855 Nonbonded interactions: 111240 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.945 3.120 nonbonded pdb=" O ILE A 19 " pdb=" O2' G G 15 " model vdw 1.982 3.040 nonbonded pdb=" OG1 THR B 126 " pdb=" OD1 ASN B 135 " model vdw 2.060 3.040 nonbonded pdb=" OH TYR H 148 " pdb=" O2' A G 7 " model vdw 2.126 3.040 nonbonded pdb=" O SER F 11 " pdb=" ND1 HIS F 14 " model vdw 2.137 3.120 ... (remaining 111235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'B' and (resid 2 through 23 or resid 33 through 120 or resid 141 through \ 214)) selection = (chain 'C' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'D' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'E' and (resid 2 through 63 or resid 76 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 39.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15074 Z= 0.293 Angle : 0.767 10.461 20421 Z= 0.434 Chirality : 0.050 0.301 2267 Planarity : 0.004 0.054 2531 Dihedral : 14.769 175.232 5807 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP F 339 HIS 0.018 0.001 HIS D 62 PHE 0.025 0.002 PHE C 166 TYR 0.021 0.002 TYR C 206 ARG 0.020 0.001 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.13583 ( 623) hydrogen bonds : angle 6.07084 ( 1833) SS BOND : bond 0.00504 ( 1) SS BOND : angle 3.27684 ( 2) covalent geometry : bond 0.00634 (15073) covalent geometry : angle 0.76608 (20419) *********************** 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 : 1.651 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: 0.3419 time to fit residues: 129.6416 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 : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 72 HIS 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 = 0.3485 r_free = 0.3485 target = 0.058761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043806 restraints weight = 78904.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045204 restraints weight = 43116.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046134 restraints weight = 29630.907| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15074 Z= 0.195 Angle : 0.676 10.119 20421 Z= 0.364 Chirality : 0.045 0.212 2267 Planarity : 0.004 0.046 2531 Dihedral : 14.140 178.889 2344 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.68 % Allowed : 9.16 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1718 helix: 1.09 (0.20), residues: 648 sheet: 0.50 (0.29), residues: 337 loop : -1.80 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 52 HIS 0.018 0.001 HIS A 72 PHE 0.018 0.002 PHE E 148 TYR 0.014 0.001 TYR F 156 ARG 0.021 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 623) hydrogen bonds : angle 5.03256 ( 1833) SS BOND : bond 0.00170 ( 1) SS BOND : angle 2.29036 ( 2) covalent geometry : bond 0.00427 (15073) covalent geometry : angle 0.67611 (20419) *********************** 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 156 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.781 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: E 147 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8208 (mm-30) REVERT: H 129 GLN cc_start: 0.7743 (mp10) cc_final: 0.7512 (mp10) REVERT: F 184 TRP cc_start: 0.9060 (t60) cc_final: 0.8835 (t60) REVERT: F 290 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9000 (tp30) REVERT: F 331 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8548 (tm-30) REVERT: F 565 PHE cc_start: 0.9209 (m-80) cc_final: 0.8632 (m-80) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 0.3141 time to fit residues: 67.0292 Evaluate side-chains 113 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 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 98 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 136 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.057920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043047 restraints weight = 80075.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044426 restraints weight = 43963.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045350 restraints weight = 30324.352| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3728 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= 0.180 Angle : 0.611 9.587 20421 Z= 0.327 Chirality : 0.044 0.317 2267 Planarity : 0.003 0.039 2531 Dihedral : 13.990 175.994 2344 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.26 % Allowed : 10.32 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1718 helix: 1.30 (0.20), residues: 648 sheet: 0.81 (0.30), residues: 324 loop : -1.72 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 52 HIS 0.014 0.001 HIS A 72 PHE 0.014 0.001 PHE E 148 TYR 0.010 0.001 TYR E 2 ARG 0.004 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 623) hydrogen bonds : angle 4.81512 ( 1833) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.91338 ( 2) covalent geometry : bond 0.00390 (15073) covalent geometry : angle 0.61073 (20419) *********************** 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 134 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.610 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: A 49 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9237 (p) REVERT: D 164 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (p0) REVERT: H 13 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7697 (pttt) REVERT: H 129 GLN cc_start: 0.8124 (mp10) cc_final: 0.7824 (mp10) REVERT: F 1 MET cc_start: 0.7732 (mmt) cc_final: 0.7299 (mmt) REVERT: F 290 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8989 (tp30) REVERT: F 565 PHE cc_start: 0.9204 (m-80) cc_final: 0.8587 (m-80) outliers start: 35 outliers final: 19 residues processed: 129 average time/residue: 0.2938 time to fit residues: 55.2208 Evaluate side-chains 108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 144 ARG 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 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 478 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 166 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 0.0020 chunk 116 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN E 92 GLN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043833 restraints weight = 79479.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045300 restraints weight = 43800.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046265 restraints weight = 30067.065| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15074 Z= 0.110 Angle : 0.554 12.365 20421 Z= 0.294 Chirality : 0.042 0.193 2267 Planarity : 0.003 0.038 2531 Dihedral : 13.761 178.126 2344 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 12.44 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1718 helix: 1.63 (0.21), residues: 648 sheet: 0.98 (0.29), residues: 324 loop : -1.61 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 184 HIS 0.006 0.001 HIS D 62 PHE 0.014 0.001 PHE E 150 TYR 0.018 0.001 TYR F 463 ARG 0.004 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 623) hydrogen bonds : angle 4.56072 ( 1833) SS BOND : bond 0.00222 ( 1) SS BOND : angle 1.49127 ( 2) covalent geometry : bond 0.00236 (15073) covalent geometry : angle 0.55397 (20419) *********************** 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 133 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.754 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: D 164 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8303 (p0) REVERT: H 13 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7668 (pttt) REVERT: H 129 GLN cc_start: 0.8191 (mp10) cc_final: 0.7903 (mp10) REVERT: F 1 MET cc_start: 0.7841 (mmt) cc_final: 0.7411 (mmt) REVERT: F 257 MET cc_start: 0.8271 (mpp) cc_final: 0.7988 (mpp) REVERT: F 290 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8962 (tp30) REVERT: F 565 PHE cc_start: 0.9224 (m-80) cc_final: 0.8643 (m-80) outliers start: 31 outliers final: 14 residues processed: 128 average time/residue: 0.2666 time to fit residues: 51.2175 Evaluate side-chains 105 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 D residue 164 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 2 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS D 125 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.055798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041106 restraints weight = 83413.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042485 restraints weight = 46075.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043380 restraints weight = 31830.999| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15074 Z= 0.256 Angle : 0.642 8.491 20421 Z= 0.343 Chirality : 0.044 0.192 2267 Planarity : 0.004 0.034 2531 Dihedral : 13.750 173.821 2344 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1718 helix: 1.37 (0.20), residues: 648 sheet: 0.75 (0.29), residues: 338 loop : -1.68 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 184 HIS 0.008 0.001 HIS D 62 PHE 0.015 0.002 PHE D 166 TYR 0.016 0.001 TYR A 180 ARG 0.012 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 623) hydrogen bonds : angle 4.78629 ( 1833) SS BOND : bond 0.00546 ( 1) SS BOND : angle 1.58082 ( 2) covalent geometry : bond 0.00554 (15073) covalent geometry : angle 0.64232 (20419) *********************** 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 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.765 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: B 88 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8064 (mmtm) REVERT: D 67 MET cc_start: 0.8099 (pmm) cc_final: 0.7385 (pmm) REVERT: D 164 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8100 (p0) REVERT: E 37 ARG cc_start: 0.9124 (mtt90) cc_final: 0.8865 (mtt90) REVERT: E 78 ARG cc_start: 0.8822 (mtt90) cc_final: 0.8566 (mtm-85) REVERT: H 13 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7841 (pttt) REVERT: H 129 GLN cc_start: 0.8458 (mp10) cc_final: 0.8211 (mp10) REVERT: F 252 PHE cc_start: 0.8928 (p90) cc_final: 0.8668 (p90) REVERT: F 264 ASP cc_start: 0.8931 (t0) cc_final: 0.8663 (t0) REVERT: F 290 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8999 (tp30) outliers start: 32 outliers final: 22 residues processed: 115 average time/residue: 0.3177 time to fit residues: 54.8584 Evaluate side-chains 105 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 D residue 164 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 35 VAL 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 H residue 187 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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 8 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** 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 = 0.3420 r_free = 0.3420 target = 0.055669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040973 restraints weight = 83522.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042374 restraints weight = 45900.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043264 restraints weight = 31556.050| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15074 Z= 0.207 Angle : 0.600 11.459 20421 Z= 0.321 Chirality : 0.043 0.177 2267 Planarity : 0.003 0.035 2531 Dihedral : 13.554 176.026 2344 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.32 % Allowed : 14.18 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1718 helix: 1.40 (0.20), residues: 648 sheet: 0.80 (0.29), residues: 324 loop : -1.66 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 184 HIS 0.008 0.001 HIS D 62 PHE 0.011 0.001 PHE D 166 TYR 0.017 0.001 TYR F 463 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 623) hydrogen bonds : angle 4.71112 ( 1833) SS BOND : bond 0.00461 ( 1) SS BOND : angle 1.52557 ( 2) covalent geometry : bond 0.00446 (15073) covalent geometry : angle 0.60009 (20419) *********************** 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: 36 poor density : 84 time to evaluate : 3.886 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: D 164 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8308 (p0) REVERT: E 103 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8357 (m-10) REVERT: E 141 ARG cc_start: 0.6497 (tpp80) cc_final: 0.6021 (tpp80) REVERT: H 13 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7776 (pttt) REVERT: H 129 GLN cc_start: 0.8562 (mp10) cc_final: 0.8277 (mp10) REVERT: F 252 PHE cc_start: 0.8925 (p90) cc_final: 0.8684 (p90) REVERT: F 264 ASP cc_start: 0.8910 (t0) cc_final: 0.8676 (t0) REVERT: F 290 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9031 (tp30) outliers start: 36 outliers final: 24 residues processed: 115 average time/residue: 0.3884 time to fit residues: 69.5122 Evaluate side-chains 105 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 2.815 ------------------------------------------------------------------------------- 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 D residue 164 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE 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 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 175 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 chunk 134 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.055821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041235 restraints weight = 82895.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042605 restraints weight = 45275.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043512 restraints weight = 31166.504| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15074 Z= 0.162 Angle : 0.577 9.950 20421 Z= 0.306 Chirality : 0.042 0.173 2267 Planarity : 0.003 0.049 2531 Dihedral : 13.483 176.341 2344 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.13 % Allowed : 14.64 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1718 helix: 1.61 (0.20), residues: 648 sheet: 0.82 (0.29), residues: 324 loop : -1.64 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 184 HIS 0.009 0.001 HIS A 72 PHE 0.014 0.001 PHE E 148 TYR 0.010 0.001 TYR H 184 ARG 0.010 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 623) hydrogen bonds : angle 4.60690 ( 1833) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.56648 ( 2) covalent geometry : bond 0.00352 (15073) covalent geometry : angle 0.57693 (20419) *********************** 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 112 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 3.901 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: D 164 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8389 (p0) REVERT: E 103 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: H 13 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7698 (pttt) REVERT: H 129 GLN cc_start: 0.8560 (mp10) cc_final: 0.8248 (mp10) REVERT: F 252 PHE cc_start: 0.8897 (p90) cc_final: 0.8632 (p90) REVERT: F 264 ASP cc_start: 0.8898 (t0) cc_final: 0.8689 (t0) REVERT: F 290 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9062 (tp30) outliers start: 33 outliers final: 23 residues processed: 107 average time/residue: 0.5592 time to fit residues: 90.7894 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 : 1.950 ------------------------------------------------------------------------------- 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 D residue 164 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE 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 5 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 H residue 211 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP 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 126 optimal weight: 0.5980 chunk 158 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS H 17 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.042422 restraints weight = 81189.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043861 restraints weight = 44415.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.044799 restraints weight = 30297.962| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15074 Z= 0.108 Angle : 0.556 11.843 20421 Z= 0.293 Chirality : 0.041 0.172 2267 Planarity : 0.003 0.041 2531 Dihedral : 13.380 178.150 2344 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.87 % Allowed : 15.09 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1718 helix: 1.81 (0.21), residues: 646 sheet: 0.93 (0.28), residues: 323 loop : -1.59 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 184 HIS 0.008 0.001 HIS A 72 PHE 0.014 0.001 PHE E 150 TYR 0.013 0.001 TYR F 463 ARG 0.006 0.000 ARG E 141 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 623) hydrogen bonds : angle 4.50917 ( 1833) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.36889 ( 2) covalent geometry : bond 0.00230 (15073) covalent geometry : angle 0.55555 (20419) *********************** 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 116 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.786 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: D 164 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8486 (p0) REVERT: H 13 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7679 (pttt) REVERT: H 129 GLN cc_start: 0.8521 (mp10) cc_final: 0.8241 (mp10) REVERT: F 1 MET cc_start: 0.8057 (mmt) cc_final: 0.7741 (mmt) REVERT: F 252 PHE cc_start: 0.8760 (p90) cc_final: 0.8433 (p90) REVERT: F 264 ASP cc_start: 0.8900 (t0) cc_final: 0.8681 (t0) REVERT: F 284 TYR cc_start: 0.8777 (t80) cc_final: 0.8491 (t80) REVERT: F 288 MET cc_start: 0.9091 (ptp) cc_final: 0.8880 (pmm) REVERT: F 290 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8976 (tp30) outliers start: 29 outliers final: 21 residues processed: 111 average time/residue: 0.2903 time to fit residues: 49.1471 Evaluate side-chains 100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 D residue 164 ASP 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 H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 432 ILE 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 130 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3430 r_free = 0.3430 target = 0.055967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.041485 restraints weight = 81866.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.042847 restraints weight = 44973.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043756 restraints weight = 30905.132| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5517 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= 0.170 Angle : 0.592 11.698 20421 Z= 0.310 Chirality : 0.042 0.173 2267 Planarity : 0.003 0.063 2531 Dihedral : 13.368 175.871 2344 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.74 % Allowed : 15.54 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1718 helix: 1.73 (0.21), residues: 649 sheet: 0.90 (0.28), residues: 323 loop : -1.58 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 184 HIS 0.009 0.001 HIS A 72 PHE 0.014 0.001 PHE E 148 TYR 0.014 0.001 TYR A 180 ARG 0.011 0.000 ARG E 144 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 623) hydrogen bonds : angle 4.61070 ( 1833) SS BOND : bond 0.00376 ( 1) SS BOND : angle 1.37369 ( 2) covalent geometry : bond 0.00368 (15073) covalent geometry : angle 0.59157 (20419) *********************** 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 106 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.742 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: D 164 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8429 (p0) REVERT: E 103 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: H 13 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7623 (pttt) REVERT: H 129 GLN cc_start: 0.8570 (mp10) cc_final: 0.8282 (mp10) REVERT: F 1 MET cc_start: 0.8092 (mmt) cc_final: 0.7781 (mmt) REVERT: F 252 PHE cc_start: 0.8889 (p90) cc_final: 0.8577 (p90) REVERT: F 264 ASP cc_start: 0.8847 (t0) cc_final: 0.8643 (t0) REVERT: F 288 MET cc_start: 0.9032 (ptp) cc_final: 0.8644 (ptp) REVERT: F 290 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9056 (tp30) outliers start: 27 outliers final: 23 residues processed: 101 average time/residue: 0.2596 time to fit residues: 40.3865 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 : 1.600 ------------------------------------------------------------------------------- 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 D residue 164 ASP Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE 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 H residue 211 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 432 ILE 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 103 optimal weight: 0.6980 chunk 169 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 168 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3462 r_free = 0.3462 target = 0.057077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042454 restraints weight = 82244.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.043875 restraints weight = 44898.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044810 restraints weight = 30665.322| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15074 Z= 0.111 Angle : 0.565 12.047 20421 Z= 0.295 Chirality : 0.041 0.182 2267 Planarity : 0.003 0.037 2531 Dihedral : 13.337 177.979 2344 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1718 helix: 1.83 (0.21), residues: 650 sheet: 0.95 (0.28), residues: 323 loop : -1.56 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 184 HIS 0.009 0.001 HIS E 72 PHE 0.013 0.001 PHE E 148 TYR 0.011 0.001 TYR A 180 ARG 0.004 0.000 ARG F 437 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 623) hydrogen bonds : angle 4.50868 ( 1833) SS BOND : bond 0.00188 ( 1) SS BOND : angle 1.31199 ( 2) covalent geometry : bond 0.00241 (15073) covalent geometry : angle 0.56527 (20419) ********************** 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 109 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8534 (p0) REVERT: H 13 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7465 (pttt) REVERT: H 129 GLN cc_start: 0.8513 (mp10) cc_final: 0.8233 (mp10) REVERT: F 1 MET cc_start: 0.8106 (mmt) cc_final: 0.7804 (mmt) REVERT: F 264 ASP cc_start: 0.8908 (t0) cc_final: 0.8691 (t0) REVERT: F 288 MET cc_start: 0.9037 (ptp) cc_final: 0.8745 (ptp) REVERT: F 290 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9033 (tp30) outliers start: 24 outliers final: 22 residues processed: 106 average time/residue: 0.2635 time to fit residues: 43.0187 Evaluate side-chains 100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 D residue 164 ASP 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 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 H residue 211 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 432 ILE 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 150 optimal weight: 4.9990 chunk 51 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3428 r_free = 0.3428 target = 0.055800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041344 restraints weight = 82797.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042695 restraints weight = 45061.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043622 restraints weight = 30832.338| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.5760 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= 0.173 Angle : 0.592 12.002 20421 Z= 0.311 Chirality : 0.042 0.197 2267 Planarity : 0.003 0.036 2531 Dihedral : 13.324 175.241 2344 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.93 % Allowed : 15.99 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1718 helix: 1.80 (0.21), residues: 647 sheet: 0.89 (0.28), residues: 323 loop : -1.55 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 184 HIS 0.009 0.001 HIS A 72 PHE 0.026 0.001 PHE H 121 TYR 0.027 0.001 TYR F 284 ARG 0.005 0.000 ARG E 144 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 623) hydrogen bonds : angle 4.60267 ( 1833) SS BOND : bond 0.00371 ( 1) SS BOND : angle 1.39845 ( 2) covalent geometry : bond 0.00376 (15073) covalent geometry : angle 0.59148 (20419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5207.96 seconds wall clock time: 94 minutes 0.99 seconds (5640.99 seconds total)