Starting phenix.real_space_refine on Fri Jul 3 06:46:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vua_65357/07_2026/9vua_65357.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 94 5.16 5 C 7981 2.51 5 N 2068 2.21 5 O 2134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12285 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 455 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 457 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 462 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 5, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2733 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2839 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2824 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 349} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2212 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain: "H" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 134 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12285 At special positions: 0 Unit cell: (112.2, 123.25, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 94 16.00 P 4 15.00 O 2134 8.00 N 2068 7.00 C 7981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 1 " - pdb=" SG CYS H 11 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 15 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 545.2 milliseconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 77.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'E' and resid 82 through 88 Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.968A pdb=" N VAL E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.935A pdb=" N PHE E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.542A pdb=" N PHE F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 111 removed outlier: 3.534A pdb=" N ASN F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.927A pdb=" N VAL F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'G' and resid 82 through 88 Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.606A pdb=" N MET G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 3.932A pdb=" N VAL G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 4.264A pdb=" N PHE G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 157 removed outlier: 3.955A pdb=" N TRP A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 200 removed outlier: 3.513A pdb=" N LEU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 4.323A pdb=" N ALA A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.589A pdb=" N ARG A 265 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.915A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.515A pdb=" N THR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 309 through 334 removed outlier: 3.812A pdb=" N VAL A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 368 through 397 Processing helix chain 'A' and resid 400 through 438 removed outlier: 3.633A pdb=" N THR A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 438 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 473 removed outlier: 3.542A pdb=" N ASN A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 157 removed outlier: 3.954A pdb=" N TRP B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 200 removed outlier: 3.687A pdb=" N LEU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.886A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 309 through 334 removed outlier: 3.714A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 368 through 397 removed outlier: 3.521A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 438 removed outlier: 3.546A pdb=" N THR B 437 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 438 " --> pdb=" O TYR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 473 removed outlier: 3.947A pdb=" N ASN B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 156 Processing helix chain 'C' and resid 164 through 200 removed outlier: 3.627A pdb=" N LEU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 224 Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.630A pdb=" N ARG C 265 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.892A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 309 through 334 removed outlier: 3.917A pdb=" N VAL C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 Processing helix chain 'C' and resid 368 through 397 Processing helix chain 'C' and resid 400 through 438 removed outlier: 3.562A pdb=" N LYS C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS C 438 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 473 removed outlier: 3.614A pdb=" N ASN C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 157 removed outlier: 3.993A pdb=" N TRP D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 200 removed outlier: 3.642A pdb=" N LEU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.548A pdb=" N ILE D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.517A pdb=" N CYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.603A pdb=" N ARG D 265 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.817A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 removed outlier: 3.555A pdb=" N ASP D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 309 through 334 removed outlier: 4.005A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.709A pdb=" N SER D 353 " --> pdb=" O MET D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 397 Processing helix chain 'H' and resid 8 through 16 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 240 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 240 Processing sheet with id=AA3, first strand: chain 'C' and resid 234 through 240 Processing sheet with id=AA4, first strand: chain 'D' and resid 234 through 240 908 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3820 1.34 - 1.46: 2371 1.46 - 1.58: 6163 1.58 - 1.70: 8 1.70 - 1.82: 152 Bond restraints: 12514 Sorted by residual: bond pdb=" C31 POV C 601 " pdb=" O31 POV C 601 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C31 POV D 601 " pdb=" O31 POV D 601 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C31 POV A 605 " pdb=" O31 POV A 605 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C21 POV C 601 " pdb=" O21 POV C 601 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 12509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 16573 2.39 - 4.79: 274 4.79 - 7.18: 29 7.18 - 9.58: 24 9.58 - 11.97: 6 Bond angle restraints: 16906 Sorted by residual: angle pdb=" N LYS D 278 " pdb=" CA LYS D 278 " pdb=" C LYS D 278 " ideal model delta sigma weight residual 111.36 104.49 6.87 1.09e+00 8.42e-01 3.98e+01 angle pdb=" N GLY E 96 " pdb=" CA GLY E 96 " pdb=" C GLY E 96 " ideal model delta sigma weight residual 115.40 107.83 7.57 1.32e+00 5.74e-01 3.29e+01 angle pdb=" N LYS E 94 " pdb=" CA LYS E 94 " pdb=" C LYS E 94 " ideal model delta sigma weight residual 112.23 105.85 6.38 1.26e+00 6.30e-01 2.56e+01 angle pdb=" C VAL G 108 " pdb=" N MET G 109 " pdb=" CA MET G 109 " ideal model delta sigma weight residual 122.11 113.96 8.15 1.64e+00 3.72e-01 2.47e+01 angle pdb=" C SER D 277 " pdb=" CA SER D 277 " pdb=" CB SER D 277 " ideal model delta sigma weight residual 109.80 115.53 -5.73 1.23e+00 6.61e-01 2.17e+01 ... (remaining 16901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 6924 24.05 - 48.09: 485 48.09 - 72.14: 54 72.14 - 96.18: 12 96.18 - 120.23: 4 Dihedral angle restraints: 7479 sinusoidal: 2937 harmonic: 4542 Sorted by residual: dihedral pdb=" CB CYS H 3 " pdb=" SG CYS H 3 " pdb=" SG CYS H 15 " pdb=" CB CYS H 15 " ideal model delta sinusoidal sigma weight residual -86.00 -160.63 74.63 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CB CYS H 1 " pdb=" SG CYS H 1 " pdb=" SG CYS H 11 " pdb=" CB CYS H 11 " ideal model delta sinusoidal sigma weight residual -86.00 -159.45 73.45 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CA HIS G 107 " pdb=" C HIS G 107 " pdb=" N VAL G 108 " pdb=" CA VAL G 108 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 7476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1436 0.038 - 0.075: 446 0.075 - 0.113: 91 0.113 - 0.150: 10 0.150 - 0.188: 5 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA LYS D 278 " pdb=" N LYS D 278 " pdb=" C LYS D 278 " pdb=" CB LYS D 278 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ASP A 340 " pdb=" N ASP A 340 " pdb=" C ASP A 340 " pdb=" CB ASP A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ASP D 255 " pdb=" N ASP D 255 " pdb=" C ASP D 255 " pdb=" CB ASP D 255 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1985 not shown) Planarity restraints: 2056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 83 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" CD GLU E 83 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU E 83 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU E 83 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 146 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C THR F 146 " 0.027 2.00e-02 2.50e+03 pdb=" O THR F 146 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA F 147 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 294 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ILE C 294 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE C 294 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 295 " -0.008 2.00e-02 2.50e+03 ... (remaining 2053 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 2837 2.79 - 3.38: 14277 3.38 - 3.96: 21666 3.96 - 4.55: 29523 4.55 - 5.14: 43204 Nonbonded interactions: 111507 Sorted by model distance: nonbonded pdb=" O LEU C 357 " pdb=" OG SER C 358 " model vdw 2.202 3.040 nonbonded pdb=" O LEU B 357 " pdb=" OG SER B 358 " model vdw 2.442 3.040 nonbonded pdb=" O HIS D 276 " pdb=" C SER D 277 " model vdw 2.447 3.270 nonbonded pdb=" O LEU C 274 " pdb=" OG SER C 277 " model vdw 2.464 3.040 nonbonded pdb=" O THR B 413 " pdb=" OG1 THR B 416 " model vdw 2.477 3.040 ... (remaining 111502 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 118 through 277 or (resid 278 and (name N or name CA or na \ me C or name O or name CB )) or resid 279 through 301 or (resid 302 and (name N \ or name CA or name C or name O or name CB )) or resid 303 through 409 or (resid \ 410 and (name N or name CA or name C or name O or name CB )) or resid 411 throug \ h 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) or \ resid 421 through 440 or (resid 441 and (name N or name CA or name C or name O o \ r name CB )) or resid 442 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 467 or (resid 468 and (name N \ or name CA or name C or name O or name CB )) or resid 469 through 472 or (resid \ 473 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 118 through 123 or (resid 124 and (name N or name CA or na \ me C or name O or name CB )) or resid 125 through 132 or (resid 133 and (name N \ or name CA or name C or name O or name CB )) or resid 134 through 204 or (resid \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 throug \ h 277 or (resid 278 and (name N or name CA or name C or name O or name CB )) or \ resid 279 through 282 or resid 296 through 409 or (resid 410 and (name N or name \ CA or name C or name O or name CB )) or resid 411 through 419 or (resid 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 through 440 o \ r (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 42 through 460 or (resid 461 and (name N or name CA or name C or name O or name \ CB )) or resid 462 through 472 or (resid 473 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'C' and (resid 118 through 123 or (resid 124 and (name N or name CA or na \ me C or name O or name CB )) or resid 125 through 132 or (resid 133 and (name N \ or name CA or name C or name O or name CB )) or resid 134 through 204 or (resid \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 throug \ h 282 or resid 296 through 301 or (resid 302 and (name N or name CA or name C or \ name O or name CB )) or resid 303 through 467 or (resid 468 and (name N or name \ CA or name C or name O or name CB )) or resid 469 through 473)) } ncs_group { reference = (chain 'E' and (resid 81 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 108 or (resid 109 and ( \ name N or name CA or name C or name O or name CB )) or resid 110 through 136 or \ (resid 137 through 140 and (name N or name CA or name C or name O or name CB )) \ or resid 141 through 144 or (resid 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 147)) selection = (chain 'F' and (resid 81 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 108 or (resid 109 and (name N or \ name CA or name C or name O or name CB )) or resid 110 through 137 or (resid 138 \ through 140 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 41 through 144 or (resid 145 and (name N or name CA or name C or name O or name \ CB )) or resid 146 through 147)) selection = (chain 'G' and (resid 81 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 98 or (resid 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 136 or (r \ esid 137 through 140 and (name N or name CA or name C or name O or name CB )) or \ resid 141 through 142 or (resid 143 and (name N or name CA or name C or name O \ or name CB )) or resid 144 through 147)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.005 0.126 12520 Z= 0.264 Angle : 0.792 11.972 16918 Z= 0.458 Chirality : 0.037 0.188 1988 Planarity : 0.003 0.027 2056 Dihedral : 15.628 120.226 4521 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.16 % Allowed : 17.59 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.22), residues: 1538 helix: 2.37 (0.16), residues: 1096 sheet: 0.79 (0.72), residues: 50 loop : -1.95 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 299 TYR 0.007 0.001 TYR D 245 PHE 0.020 0.001 PHE B 455 TRP 0.012 0.001 TRP A 327 HIS 0.002 0.001 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.26 (12514) covalent geometry : angle 0.79187 / 0.46 (16906) SS BOND : bond 0.00246 / 0.13 ( 6) SS BOND : angle 0.63735 / 0.50 ( 12) hydrogen bonds : bond 0.14881 / 10.40 ( 908) hydrogen bonds : angle 4.94542 / 3.63 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: E 83 GLU cc_start: 0.7240 (mp0) cc_final: 0.6729 (mp0) REVERT: F 145 MET cc_start: 0.3740 (ttt) cc_final: 0.3520 (ttp) REVERT: A 136 ASP cc_start: 0.8230 (t70) cc_final: 0.8001 (t0) REVERT: A 137 TYR cc_start: 0.8216 (m-80) cc_final: 0.7829 (m-80) REVERT: A 411 MET cc_start: 0.8287 (mmm) cc_final: 0.8045 (mmm) REVERT: A 464 SER cc_start: 0.8096 (m) cc_final: 0.7842 (p) REVERT: B 282 ASP cc_start: 0.8092 (m-30) cc_final: 0.7720 (p0) REVERT: B 377 LEU cc_start: 0.8530 (mt) cc_final: 0.8290 (tp) REVERT: B 408 ASN cc_start: 0.8141 (m110) cc_final: 0.7913 (m-40) REVERT: C 194 GLN cc_start: 0.7589 (tt0) cc_final: 0.6830 (tm-30) REVERT: C 199 ASP cc_start: 0.7806 (t0) cc_final: 0.7374 (t0) REVERT: C 209 MET cc_start: 0.7695 (mmm) cc_final: 0.7290 (mmm) REVERT: C 381 MET cc_start: 0.8604 (mmt) cc_final: 0.8366 (mmt) REVERT: D 302 MET cc_start: 0.7646 (ppp) cc_final: 0.7334 (ppp) REVERT: D 340 ASP cc_start: 0.7818 (t0) cc_final: 0.7405 (t0) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.1019 time to fit residues: 37.0819 Evaluate side-chains 212 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN B 367 ASN C 123 HIS C 339 GLN ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN D 276 HIS D 367 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108796 restraints weight = 15077.152| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.08 r_work: 0.3027 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12520 Z= 0.215 Angle : 0.562 6.481 16918 Z= 0.304 Chirality : 0.039 0.152 1988 Planarity : 0.004 0.027 2056 Dihedral : 9.669 103.581 1824 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.01 % Allowed : 17.75 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.22), residues: 1538 helix: 2.64 (0.15), residues: 1122 sheet: 0.65 (0.67), residues: 54 loop : -1.29 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 125 TYR 0.022 0.002 TYR C 361 PHE 0.019 0.002 PHE D 356 TRP 0.027 0.002 TRP B 205 HIS 0.007 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (12514) covalent geometry : angle 0.56186 / 0.30 (16906) SS BOND : bond 0.00608 / 0.32 ( 6) SS BOND : angle 0.98746 / 0.72 ( 12) hydrogen bonds : bond 0.06976 / 4.94 ( 908) hydrogen bonds : angle 3.64112 / 2.68 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 216 PHE cc_start: 0.7299 (m-10) cc_final: 0.6860 (m-10) REVERT: A 436 ASN cc_start: 0.7512 (t0) cc_final: 0.7301 (t0) REVERT: A 464 SER cc_start: 0.8009 (m) cc_final: 0.7751 (p) REVERT: B 197 MET cc_start: 0.7161 (mmm) cc_final: 0.6898 (mmm) REVERT: B 279 LEU cc_start: 0.7404 (mt) cc_final: 0.7172 (mp) REVERT: B 282 ASP cc_start: 0.7796 (m-30) cc_final: 0.7157 (p0) REVERT: B 377 LEU cc_start: 0.8357 (mt) cc_final: 0.8125 (tp) REVERT: B 467 MET cc_start: 0.7720 (tpp) cc_final: 0.7473 (tpp) REVERT: B 469 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 471 LYS cc_start: 0.8745 (tptt) cc_final: 0.8178 (tppt) REVERT: C 209 MET cc_start: 0.7787 (mmm) cc_final: 0.7385 (mmm) REVERT: C 219 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8181 (tp) REVERT: C 296 PHE cc_start: 0.7855 (m-80) cc_final: 0.7568 (m-80) REVERT: C 334 ARG cc_start: 0.8725 (ttp-170) cc_final: 0.8522 (ptt180) REVERT: C 381 MET cc_start: 0.8525 (mmt) cc_final: 0.8268 (mmt) REVERT: D 137 TYR cc_start: 0.8230 (m-80) cc_final: 0.7916 (m-80) REVERT: D 302 MET cc_start: 0.7503 (ppp) cc_final: 0.7157 (ppp) REVERT: D 340 ASP cc_start: 0.8020 (t0) cc_final: 0.7660 (t70) outliers start: 38 outliers final: 24 residues processed: 237 average time/residue: 0.0890 time to fit residues: 32.0441 Evaluate side-chains 215 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 254 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 11 optimal weight: 0.0050 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 149 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 339 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.195519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116977 restraints weight = 15266.667| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.53 r_work: 0.3084 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12520 Z= 0.109 Angle : 0.440 7.993 16918 Z= 0.237 Chirality : 0.035 0.166 1988 Planarity : 0.003 0.024 2056 Dihedral : 8.669 82.060 1822 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.46 % Allowed : 18.94 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.22), residues: 1538 helix: 3.20 (0.15), residues: 1122 sheet: 0.23 (0.67), residues: 58 loop : -0.85 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 125 TYR 0.007 0.001 TYR A 233 PHE 0.010 0.001 PHE B 455 TRP 0.021 0.001 TRP B 205 HIS 0.004 0.000 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (12514) covalent geometry : angle 0.43994 / 0.24 (16906) SS BOND : bond 0.00084 / 0.05 ( 6) SS BOND : angle 0.88199 / 0.59 ( 12) hydrogen bonds : bond 0.04919 / 3.46 ( 908) hydrogen bonds : angle 3.21409 / 2.38 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 253 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7734 (p0) REVERT: A 464 SER cc_start: 0.7852 (m) cc_final: 0.7599 (p) REVERT: A 469 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7618 (tp-100) REVERT: B 197 MET cc_start: 0.7116 (mmm) cc_final: 0.6856 (mmm) REVERT: B 282 ASP cc_start: 0.7756 (m-30) cc_final: 0.7176 (p0) REVERT: B 377 LEU cc_start: 0.8286 (mt) cc_final: 0.8056 (tp) REVERT: B 467 MET cc_start: 0.7520 (tpp) cc_final: 0.7296 (tpp) REVERT: B 471 LYS cc_start: 0.8685 (tptt) cc_final: 0.8112 (tppt) REVERT: C 194 GLN cc_start: 0.7379 (tt0) cc_final: 0.6671 (tm-30) REVERT: C 209 MET cc_start: 0.7579 (mmm) cc_final: 0.7269 (mmm) REVERT: C 296 PHE cc_start: 0.7828 (m-80) cc_final: 0.7509 (m-80) REVERT: C 381 MET cc_start: 0.8453 (mmt) cc_final: 0.8216 (mmt) REVERT: D 302 MET cc_start: 0.7351 (ppp) cc_final: 0.7050 (ppp) REVERT: D 340 ASP cc_start: 0.7984 (t0) cc_final: 0.7693 (t70) outliers start: 31 outliers final: 15 residues processed: 224 average time/residue: 0.0870 time to fit residues: 29.3397 Evaluate side-chains 210 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 254 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 106 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120215 restraints weight = 15113.634| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.72 r_work: 0.3079 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12520 Z= 0.103 Angle : 0.430 7.793 16918 Z= 0.229 Chirality : 0.035 0.141 1988 Planarity : 0.002 0.024 2056 Dihedral : 8.364 78.823 1822 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.46 % Allowed : 18.70 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.22), residues: 1538 helix: 3.43 (0.15), residues: 1109 sheet: 0.13 (0.67), residues: 60 loop : -0.61 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.019 0.001 TYR A 188 PHE 0.013 0.001 PHE B 409 TRP 0.016 0.001 TRP B 205 HIS 0.002 0.001 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (12514) covalent geometry : angle 0.42985 / 0.23 (16906) SS BOND : bond 0.00154 / 0.08 ( 6) SS BOND : angle 0.65493 / 0.47 ( 12) hydrogen bonds : bond 0.04599 / 3.24 ( 908) hydrogen bonds : angle 3.06741 / 2.27 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 253 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 408 ASN cc_start: 0.8812 (m-40) cc_final: 0.8584 (m-40) REVERT: A 464 SER cc_start: 0.7935 (m) cc_final: 0.7666 (p) REVERT: A 469 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7583 (tp-100) REVERT: B 241 LEU cc_start: 0.8364 (mp) cc_final: 0.8112 (mt) REVERT: B 282 ASP cc_start: 0.7771 (m-30) cc_final: 0.7133 (p0) REVERT: B 377 LEU cc_start: 0.8487 (mt) cc_final: 0.8262 (tp) REVERT: C 194 GLN cc_start: 0.7467 (tt0) cc_final: 0.6781 (tm-30) REVERT: C 206 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7954 (mtm180) REVERT: C 209 MET cc_start: 0.7528 (mmm) cc_final: 0.7147 (mmm) REVERT: C 381 MET cc_start: 0.8580 (mmt) cc_final: 0.8348 (mmt) REVERT: D 302 MET cc_start: 0.7410 (ppp) cc_final: 0.7102 (ppp) REVERT: D 340 ASP cc_start: 0.8091 (t0) cc_final: 0.7824 (t70) outliers start: 31 outliers final: 19 residues processed: 225 average time/residue: 0.0956 time to fit residues: 32.2308 Evaluate side-chains 216 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 254 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 110 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.0000 chunk 118 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN B 469 GLN D 123 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110563 restraints weight = 15128.478| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.31 r_work: 0.3009 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12520 Z= 0.157 Angle : 0.487 7.684 16918 Z= 0.260 Chirality : 0.037 0.151 1988 Planarity : 0.003 0.024 2056 Dihedral : 8.786 82.817 1822 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.69 % Allowed : 19.41 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.22), residues: 1538 helix: 3.15 (0.15), residues: 1122 sheet: 1.43 (0.71), residues: 50 loop : -0.53 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 13 TYR 0.015 0.001 TYR B 361 PHE 0.016 0.001 PHE B 356 TRP 0.018 0.002 TRP B 205 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12514) covalent geometry : angle 0.48701 / 0.26 (16906) SS BOND : bond 0.00782 / 0.51 ( 6) SS BOND : angle 0.60069 / 0.36 ( 12) hydrogen bonds : bond 0.05884 / 4.16 ( 908) hydrogen bonds : angle 3.23051 / 2.38 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 ASP cc_start: 0.5121 (OUTLIER) cc_final: 0.4838 (p0) REVERT: A 253 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 408 ASN cc_start: 0.8814 (m-40) cc_final: 0.8590 (m-40) REVERT: A 464 SER cc_start: 0.7858 (m) cc_final: 0.7598 (p) REVERT: A 469 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7598 (tp-100) REVERT: B 282 ASP cc_start: 0.7669 (m-30) cc_final: 0.6997 (p0) REVERT: B 377 LEU cc_start: 0.8397 (mt) cc_final: 0.8180 (tp) REVERT: C 209 MET cc_start: 0.7675 (mmm) cc_final: 0.7467 (mmm) REVERT: D 302 MET cc_start: 0.7432 (ppp) cc_final: 0.7111 (ppp) REVERT: D 340 ASP cc_start: 0.8175 (t0) cc_final: 0.7894 (t70) outliers start: 34 outliers final: 23 residues processed: 223 average time/residue: 0.0980 time to fit residues: 32.6190 Evaluate side-chains 219 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115052 restraints weight = 15135.622| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.49 r_work: 0.3002 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12520 Z= 0.136 Angle : 0.464 8.407 16918 Z= 0.246 Chirality : 0.036 0.229 1988 Planarity : 0.003 0.025 2056 Dihedral : 8.731 81.051 1822 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.46 % Allowed : 19.73 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.22), residues: 1538 helix: 3.11 (0.15), residues: 1134 sheet: 1.28 (0.73), residues: 50 loop : -0.44 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 125 TYR 0.022 0.001 TYR A 188 PHE 0.013 0.001 PHE B 356 TRP 0.016 0.001 TRP B 205 HIS 0.003 0.001 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12514) covalent geometry : angle 0.46322 / 0.25 (16906) SS BOND : bond 0.00343 / 0.19 ( 6) SS BOND : angle 0.82829 / 0.60 ( 12) hydrogen bonds : bond 0.05446 / 3.84 ( 908) hydrogen bonds : angle 3.15733 / 2.33 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 ASP cc_start: 0.5160 (OUTLIER) cc_final: 0.4869 (p0) REVERT: G 99 TYR cc_start: 0.3940 (OUTLIER) cc_final: 0.3483 (m-80) REVERT: A 253 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7978 (p0) REVERT: A 464 SER cc_start: 0.8018 (m) cc_final: 0.7744 (p) REVERT: B 282 ASP cc_start: 0.7706 (m-30) cc_final: 0.7227 (p0) REVERT: B 377 LEU cc_start: 0.8533 (mt) cc_final: 0.8324 (tp) REVERT: C 209 MET cc_start: 0.7765 (mmm) cc_final: 0.7422 (mmm) REVERT: C 381 MET cc_start: 0.8656 (mmt) cc_final: 0.8404 (mmt) REVERT: D 302 MET cc_start: 0.7468 (ppp) cc_final: 0.7154 (ppp) REVERT: D 340 ASP cc_start: 0.8265 (t0) cc_final: 0.7979 (t70) outliers start: 31 outliers final: 20 residues processed: 220 average time/residue: 0.0873 time to fit residues: 29.2091 Evaluate side-chains 217 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118503 restraints weight = 15065.071| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.47 r_work: 0.3041 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12520 Z= 0.104 Angle : 0.436 8.999 16918 Z= 0.231 Chirality : 0.034 0.157 1988 Planarity : 0.002 0.026 2056 Dihedral : 8.425 82.866 1822 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.61 % Allowed : 19.10 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.22), residues: 1538 helix: 3.23 (0.15), residues: 1147 sheet: 1.43 (0.75), residues: 50 loop : -0.32 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 125 TYR 0.019 0.001 TYR A 188 PHE 0.009 0.001 PHE B 356 TRP 0.019 0.001 TRP B 205 HIS 0.001 0.000 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (12514) covalent geometry : angle 0.43581 / 0.23 (16906) SS BOND : bond 0.00178 / 0.11 ( 6) SS BOND : angle 0.57724 / 0.38 ( 12) hydrogen bonds : bond 0.04591 / 3.23 ( 908) hydrogen bonds : angle 3.02643 / 2.24 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 99 TYR cc_start: 0.3953 (OUTLIER) cc_final: 0.3534 (m-80) REVERT: A 253 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7935 (p0) REVERT: A 464 SER cc_start: 0.7911 (m) cc_final: 0.7683 (p) REVERT: B 282 ASP cc_start: 0.7539 (m-30) cc_final: 0.7066 (p0) REVERT: B 377 LEU cc_start: 0.8511 (mt) cc_final: 0.8301 (tp) REVERT: C 209 MET cc_start: 0.7653 (mmm) cc_final: 0.7327 (mmm) REVERT: C 381 MET cc_start: 0.8594 (mmt) cc_final: 0.8321 (mmt) REVERT: D 302 MET cc_start: 0.7413 (ppp) cc_final: 0.7136 (ppp) REVERT: D 340 ASP cc_start: 0.8218 (t0) cc_final: 0.7937 (t0) REVERT: H 11 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7147 (t) outliers start: 33 outliers final: 21 residues processed: 223 average time/residue: 0.0853 time to fit residues: 28.8274 Evaluate side-chains 215 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain H residue 11 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114329 restraints weight = 15061.655| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.44 r_work: 0.2987 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12520 Z= 0.163 Angle : 0.506 10.117 16918 Z= 0.265 Chirality : 0.038 0.362 1988 Planarity : 0.003 0.032 2056 Dihedral : 8.863 86.512 1822 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.61 % Allowed : 19.73 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.22), residues: 1538 helix: 3.03 (0.15), residues: 1147 sheet: 1.36 (0.73), residues: 50 loop : -0.43 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 125 TYR 0.013 0.001 TYR D 245 PHE 0.016 0.001 PHE B 356 TRP 0.015 0.001 TRP B 205 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (12514) covalent geometry : angle 0.50577 / 0.26 (16906) SS BOND : bond 0.00462 / 0.25 ( 6) SS BOND : angle 0.64344 / 0.40 ( 12) hydrogen bonds : bond 0.05872 / 4.15 ( 908) hydrogen bonds : angle 3.19555 / 2.36 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 83 GLU cc_start: 0.6919 (mp0) cc_final: 0.6705 (mp0) REVERT: F 95 ASP cc_start: 0.5131 (OUTLIER) cc_final: 0.4898 (p0) REVERT: G 99 TYR cc_start: 0.3994 (OUTLIER) cc_final: 0.3557 (m-80) REVERT: A 253 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8128 (p0) REVERT: A 408 ASN cc_start: 0.8808 (m-40) cc_final: 0.8587 (m110) REVERT: A 464 SER cc_start: 0.8024 (m) cc_final: 0.7759 (p) REVERT: B 282 ASP cc_start: 0.7534 (m-30) cc_final: 0.7031 (p0) REVERT: C 209 MET cc_start: 0.7886 (mmm) cc_final: 0.7527 (mmm) REVERT: D 302 MET cc_start: 0.7537 (ppp) cc_final: 0.7229 (ppp) REVERT: D 340 ASP cc_start: 0.8314 (t0) cc_final: 0.8048 (t70) outliers start: 33 outliers final: 27 residues processed: 221 average time/residue: 0.0884 time to fit residues: 29.5788 Evaluate side-chains 221 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 74 optimal weight: 0.0000 chunk 48 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 GLN D 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.192298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117247 restraints weight = 15091.422| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.63 r_work: 0.3013 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12520 Z= 0.122 Angle : 0.475 9.023 16918 Z= 0.247 Chirality : 0.036 0.300 1988 Planarity : 0.003 0.030 2056 Dihedral : 8.573 88.082 1822 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 20.44 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.22), residues: 1538 helix: 3.14 (0.15), residues: 1147 sheet: 1.13 (0.74), residues: 52 loop : -0.34 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 125 TYR 0.020 0.001 TYR A 188 PHE 0.012 0.001 PHE B 356 TRP 0.018 0.001 TRP B 205 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12514) covalent geometry : angle 0.47472 / 0.25 (16906) SS BOND : bond 0.00227 / 0.12 ( 6) SS BOND : angle 0.56341 / 0.35 ( 12) hydrogen bonds : bond 0.05110 / 3.61 ( 908) hydrogen bonds : angle 3.11834 / 2.30 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 83 GLU cc_start: 0.6933 (mp0) cc_final: 0.6728 (mp0) REVERT: F 95 ASP cc_start: 0.4973 (OUTLIER) cc_final: 0.4750 (p0) REVERT: G 99 TYR cc_start: 0.4053 (OUTLIER) cc_final: 0.3606 (m-80) REVERT: A 253 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8025 (p0) REVERT: A 408 ASN cc_start: 0.8734 (m-40) cc_final: 0.8511 (m110) REVERT: A 464 SER cc_start: 0.7943 (m) cc_final: 0.7680 (p) REVERT: B 137 TYR cc_start: 0.7709 (m-80) cc_final: 0.7464 (m-80) REVERT: B 282 ASP cc_start: 0.7444 (m-30) cc_final: 0.6984 (p0) REVERT: C 209 MET cc_start: 0.7784 (mmm) cc_final: 0.7425 (mmm) REVERT: D 302 MET cc_start: 0.7480 (ppp) cc_final: 0.7181 (ppp) REVERT: D 340 ASP cc_start: 0.8231 (t0) cc_final: 0.7952 (t0) outliers start: 27 outliers final: 23 residues processed: 214 average time/residue: 0.0884 time to fit residues: 28.5185 Evaluate side-chains 218 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118857 restraints weight = 15228.994| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.70 r_work: 0.3031 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12520 Z= 0.113 Angle : 0.472 10.911 16918 Z= 0.244 Chirality : 0.036 0.285 1988 Planarity : 0.003 0.040 2056 Dihedral : 8.303 88.415 1822 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.06 % Allowed : 20.52 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.22), residues: 1538 helix: 3.21 (0.15), residues: 1147 sheet: 1.47 (0.75), residues: 50 loop : -0.28 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 125 TYR 0.009 0.001 TYR B 361 PHE 0.016 0.001 PHE A 409 TRP 0.019 0.001 TRP B 205 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12514) covalent geometry : angle 0.47157 / 0.24 (16906) SS BOND : bond 0.00232 / 0.13 ( 6) SS BOND : angle 0.48245 / 0.30 ( 12) hydrogen bonds : bond 0.04784 / 3.37 ( 908) hydrogen bonds : angle 3.05081 / 2.26 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 ASP cc_start: 0.4999 (OUTLIER) cc_final: 0.4785 (p0) REVERT: G 99 TYR cc_start: 0.4013 (OUTLIER) cc_final: 0.3612 (m-80) REVERT: A 137 TYR cc_start: 0.8175 (m-80) cc_final: 0.7793 (m-80) REVERT: A 253 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8003 (p0) REVERT: A 408 ASN cc_start: 0.8725 (m-40) cc_final: 0.8500 (m110) REVERT: A 464 SER cc_start: 0.7900 (m) cc_final: 0.7623 (p) REVERT: B 282 ASP cc_start: 0.7497 (m-30) cc_final: 0.7088 (p0) REVERT: B 469 GLN cc_start: 0.8492 (tp40) cc_final: 0.8286 (tp-100) REVERT: C 209 MET cc_start: 0.7695 (mmm) cc_final: 0.7305 (mmm) REVERT: D 298 THR cc_start: 0.7689 (m) cc_final: 0.7285 (p) REVERT: D 302 MET cc_start: 0.7429 (ppp) cc_final: 0.7140 (ppp) REVERT: D 340 ASP cc_start: 0.8227 (t0) cc_final: 0.7944 (t0) outliers start: 26 outliers final: 22 residues processed: 213 average time/residue: 0.0851 time to fit residues: 27.6989 Evaluate side-chains 217 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.193008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118413 restraints weight = 14992.269| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.64 r_work: 0.3031 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12520 Z= 0.115 Angle : 0.472 11.116 16918 Z= 0.245 Chirality : 0.036 0.275 1988 Planarity : 0.003 0.037 2056 Dihedral : 8.201 89.176 1822 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 20.52 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.22), residues: 1538 helix: 3.24 (0.15), residues: 1145 sheet: 1.48 (0.75), residues: 50 loop : -0.28 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 125 TYR 0.019 0.001 TYR A 188 PHE 0.014 0.001 PHE A 409 TRP 0.017 0.001 TRP B 205 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12514) covalent geometry : angle 0.47248 / 0.25 (16906) SS BOND : bond 0.00235 / 0.13 ( 6) SS BOND : angle 0.48017 / 0.29 ( 12) hydrogen bonds : bond 0.04798 / 3.38 ( 908) hydrogen bonds : angle 3.04390 / 2.25 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4156.04 seconds wall clock time: 71 minutes 25.19 seconds (4285.19 seconds total)