Starting phenix.real_space_refine on Thu Jul 2 21:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jru_36606/07_2026/8jru_36606.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3992 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 17 5.16 5 C 4571 2.51 5 N 1199 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 7120 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2008 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 4, 'TRANS': 262} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 6, 'HIS:plan': 2, 'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2576 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 28, 'TRANS': 317} Chain breaks: 3 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 109 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 891 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.64, per 1000 atoms: 0.23 Number of scatterers: 7120 At special positions: 0 Unit cell: (73.899, 92.106, 154.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 8 15.00 O 1325 8.00 N 1199 7.00 C 4571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 336.1 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 14 sheets defined 26.4% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 139 through 165 removed outlier: 3.555A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR R 145 " --> pdb=" O PHE R 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 201 removed outlier: 3.851A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 254 removed outlier: 4.172A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 273 removed outlier: 4.254A pdb=" N SER R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 285 removed outlier: 3.653A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 304 removed outlier: 4.141A pdb=" N PHE R 303 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 335 removed outlier: 4.459A pdb=" N VAL R 311 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN R 327 " --> pdb=" O VAL R 323 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 367 removed outlier: 3.616A pdb=" N LEU R 347 " --> pdb=" O TYR R 343 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR R 353 " --> pdb=" O LYS R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix removed outlier: 3.588A pdb=" N GLU R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 363 " --> pdb=" O GLY R 359 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 367 " --> pdb=" O VAL R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 385 removed outlier: 3.503A pdb=" N ASP R 385 " --> pdb=" O LYS R 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 381 through 385' Processing helix chain 'R' and resid 385 through 391 removed outlier: 4.101A pdb=" N SER R 389 " --> pdb=" O ASP R 385 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER R 390 " --> pdb=" O LEU R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 424 removed outlier: 3.641A pdb=" N GLN R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.566A pdb=" N GLU A 50 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.298A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.055A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'R' and resid 1361 through 1364 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.645A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.934A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 63 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 75 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.934A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.764A pdb=" N ALA A 184 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 201 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 199 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 198 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 221 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 266 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 4.255A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 328 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 258 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.574A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 7.111A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.731A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.824A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.631A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 72 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AB5, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.137A pdb=" N THR B 108 " --> pdb=" O TYR B 93 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 798 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: 1.03 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1189 1.32 - 1.45: 1971 1.45 - 1.57: 4072 1.57 - 1.69: 23 1.69 - 1.81: 26 Bond restraints: 7281 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O5 PIO A 701 " pdb=" P5 PIO A 701 " ideal model delta sigma weight residual 1.699 1.601 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O1P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C4 PIO A 701 " pdb=" O4 PIO A 701 " ideal model delta sigma weight residual 1.389 1.474 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O2P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 7276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 9910 4.19 - 8.38: 28 8.38 - 12.57: 12 12.57 - 16.76: 0 16.76 - 20.95: 1 Bond angle restraints: 9951 Sorted by residual: angle pdb=" C1 PIO A 701 " pdb=" O1 PIO A 701 " pdb=" P1 PIO A 701 " ideal model delta sigma weight residual 122.39 143.34 -20.95 3.00e+00 1.11e-01 4.88e+01 angle pdb=" CB TPO R1360 " pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 119.31 106.98 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O1 PIO A 701 " pdb=" P1 PIO A 701 " pdb=" O13 PIO A 701 " ideal model delta sigma weight residual 97.64 109.31 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C3C PIO A 701 " pdb=" C2C PIO A 701 " pdb=" O2C PIO A 701 " ideal model delta sigma weight residual 108.19 119.57 -11.38 3.00e+00 1.11e-01 1.44e+01 ... (remaining 9946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3785 17.95 - 35.90: 355 35.90 - 53.85: 73 53.85 - 71.80: 7 71.80 - 89.74: 8 Dihedral angle restraints: 4228 sinusoidal: 1480 harmonic: 2748 Sorted by residual: dihedral pdb=" CA LEU A 243 " pdb=" C LEU A 243 " pdb=" N PHE A 244 " pdb=" CA PHE A 244 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CG ARG R 412 " pdb=" CD ARG R 412 " pdb=" NE ARG R 412 " pdb=" CZ ARG R 412 " ideal model delta sinusoidal sigma weight residual 90.00 131.84 -41.84 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CA LEU H 89 " pdb=" CB LEU H 89 " pdb=" CG LEU H 89 " pdb=" CD1 LEU H 89 " ideal model delta sinusoidal sigma weight residual 60.00 119.13 -59.13 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1098 0.094 - 0.188: 66 0.188 - 0.282: 0 0.282 - 0.375: 0 0.375 - 0.469: 1 Chirality restraints: 1165 Sorted by residual: chirality pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" C3C PIO A 701 " pdb=" O2C PIO A 701 " both_signs ideal model delta sigma weight residual False -2.56 -2.09 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CB VAL R 292 " pdb=" CA VAL R 292 " pdb=" CG1 VAL R 292 " pdb=" CG2 VAL R 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CG LEU B 102 " pdb=" CB LEU B 102 " pdb=" CD1 LEU B 102 " pdb=" CD2 LEU B 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1162 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 76 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASN B 76 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN B 76 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 77 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C THR B 56 " -0.031 2.00e-02 2.50e+03 pdb=" O THR B 56 " 0.012 2.00e-02 2.50e+03 pdb=" N THR B 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 44 " -0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 45 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.024 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1208 2.77 - 3.30: 6500 3.30 - 3.84: 11246 3.84 - 4.37: 12090 4.37 - 4.90: 22122 Nonbonded interactions: 53166 Sorted by model distance: nonbonded pdb=" OH TYR A 238 " pdb=" OE2 GLU A 346 " model vdw 2.241 3.040 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP A 204 " pdb=" OG SER A 215 " model vdw 2.273 3.040 nonbonded pdb=" N GLU R 406 " pdb=" OE1 GLU R 406 " model vdw 2.304 3.120 nonbonded pdb=" N VAL H 5 " pdb=" O SER H 28 " model vdw 2.332 3.120 ... (remaining 53161 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.004 0.107 7281 Z= 0.184 Angle : 0.689 20.947 9951 Z= 0.295 Chirality : 0.042 0.469 1165 Planarity : 0.004 0.043 1244 Dihedral : 14.840 89.745 2458 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.29 % Allowed : 12.86 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.29), residues: 912 helix: 1.45 (0.37), residues: 199 sheet: 1.00 (0.34), residues: 273 loop : -0.76 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 173 TYR 0.008 0.001 TYR B 79 PHE 0.016 0.001 PHE A 244 TRP 0.010 0.001 TRP R 295 HIS 0.008 0.000 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 7281) covalent geometry : angle 0.68907 / 0.29 ( 9951) hydrogen bonds : bond 0.28405 / 19.31 ( 277) hydrogen bonds : angle 9.43441 / 7.00 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.282 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.0598 time to fit residues: 10.0517 Evaluate side-chains 110 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN L 91 GLN B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106397 restraints weight = 12988.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107259 restraints weight = 9765.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108272 restraints weight = 8025.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108647 restraints weight = 6284.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109071 restraints weight = 5949.376| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7281 Z= 0.149 Angle : 0.591 7.808 9951 Z= 0.297 Chirality : 0.043 0.156 1165 Planarity : 0.004 0.036 1244 Dihedral : 6.397 86.001 1043 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 2.57 % Allowed : 13.29 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.29), residues: 912 helix: 1.76 (0.36), residues: 215 sheet: 0.87 (0.33), residues: 277 loop : -0.99 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.011 0.001 TYR H 107 PHE 0.023 0.001 PHE R 278 TRP 0.008 0.001 TRP R 415 HIS 0.005 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7281) covalent geometry : angle 0.59057 / 0.30 ( 9951) hydrogen bonds : bond 0.05136 / 3.44 ( 277) hydrogen bonds : angle 6.07608 / 4.46 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: R 410 GLU cc_start: 0.8073 (tp30) cc_final: 0.7771 (tm-30) REVERT: A 154 LEU cc_start: 0.7775 (tp) cc_final: 0.7495 (tp) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.0666 time to fit residues: 12.2664 Evaluate side-chains 113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 357 LEU Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.100620 restraints weight = 12962.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101338 restraints weight = 10135.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102138 restraints weight = 8648.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102948 restraints weight = 6748.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103115 restraints weight = 6259.685| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7281 Z= 0.195 Angle : 0.634 8.179 9951 Z= 0.320 Chirality : 0.044 0.166 1165 Planarity : 0.004 0.037 1244 Dihedral : 6.408 85.392 1039 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 4.43 % Allowed : 14.29 % Favored : 81.29 % 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: 0.02 (0.29), residues: 912 helix: 1.45 (0.36), residues: 212 sheet: 0.37 (0.32), residues: 298 loop : -1.03 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.017 0.001 TYR H 107 PHE 0.033 0.002 PHE L 84 TRP 0.048 0.003 TRP R 305 HIS 0.008 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 7281) covalent geometry : angle 0.63400 / 0.32 ( 9951) hydrogen bonds : bond 0.04675 / 3.14 ( 277) hydrogen bonds : angle 5.39969 / 3.99 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.164 Fit side-chains REVERT: R 410 GLU cc_start: 0.8262 (tp30) cc_final: 0.7814 (tm-30) REVERT: H 106 TRP cc_start: 0.5986 (OUTLIER) cc_final: 0.4131 (t-100) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.0705 time to fit residues: 12.3198 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 0.0070 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS A 299 ASN H 42 GLN B 44 HIS B 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.102868 restraints weight = 13014.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103589 restraints weight = 9796.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104543 restraints weight = 8352.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105010 restraints weight = 6431.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105747 restraints weight = 6040.885| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7281 Z= 0.106 Angle : 0.566 8.488 9951 Z= 0.282 Chirality : 0.041 0.179 1165 Planarity : 0.004 0.048 1244 Dihedral : 6.150 82.468 1039 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.19 % Rotamer: Outliers : 2.57 % Allowed : 16.29 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 912 helix: 1.58 (0.36), residues: 216 sheet: 0.35 (0.31), residues: 302 loop : -1.02 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 173 TYR 0.018 0.001 TYR B 79 PHE 0.031 0.001 PHE L 84 TRP 0.030 0.002 TRP R 305 HIS 0.008 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 7281) covalent geometry : angle 0.56568 / 0.28 ( 9951) hydrogen bonds : bond 0.03690 / 2.47 ( 277) hydrogen bonds : angle 4.97482 / 3.64 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: R 343 TYR cc_start: 0.7223 (t80) cc_final: 0.6825 (t80) REVERT: R 410 GLU cc_start: 0.8198 (tp30) cc_final: 0.7812 (tm-30) REVERT: B 34 MET cc_start: 0.8196 (mmt) cc_final: 0.7644 (mmt) REVERT: B 79 TYR cc_start: 0.7357 (m-80) cc_final: 0.6911 (m-80) outliers start: 18 outliers final: 10 residues processed: 116 average time/residue: 0.0710 time to fit residues: 11.6064 Evaluate side-chains 105 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain L residue 18 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 0.0370 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101633 restraints weight = 13054.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102639 restraints weight = 9440.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103620 restraints weight = 7830.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104151 restraints weight = 6049.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104478 restraints weight = 5732.144| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7281 Z= 0.119 Angle : 0.564 9.226 9951 Z= 0.280 Chirality : 0.041 0.169 1165 Planarity : 0.004 0.036 1244 Dihedral : 6.047 81.110 1039 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 3.00 % Allowed : 17.14 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.29), residues: 912 helix: 1.67 (0.36), residues: 211 sheet: 0.33 (0.31), residues: 302 loop : -1.05 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 173 TYR 0.019 0.001 TYR B 79 PHE 0.029 0.001 PHE L 84 TRP 0.023 0.001 TRP R 305 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7281) covalent geometry : angle 0.56377 / 0.28 ( 9951) hydrogen bonds : bond 0.03656 / 2.42 ( 277) hydrogen bonds : angle 4.82354 / 3.52 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: R 343 TYR cc_start: 0.7324 (t80) cc_final: 0.6906 (t80) REVERT: R 410 GLU cc_start: 0.8229 (tp30) cc_final: 0.7818 (tm-30) REVERT: B 34 MET cc_start: 0.8234 (mmt) cc_final: 0.7746 (mmt) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 0.0746 time to fit residues: 12.1378 Evaluate side-chains 108 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS A 299 ASN B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101502 restraints weight = 13277.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102395 restraints weight = 10060.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103248 restraints weight = 8198.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103945 restraints weight = 6596.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104110 restraints weight = 6178.113| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7281 Z= 0.131 Angle : 0.579 10.088 9951 Z= 0.289 Chirality : 0.042 0.169 1165 Planarity : 0.004 0.041 1244 Dihedral : 6.018 79.795 1039 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 3.29 % Allowed : 17.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.29), residues: 912 helix: 1.75 (0.36), residues: 211 sheet: 0.36 (0.32), residues: 300 loop : -1.07 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 173 TYR 0.013 0.001 TYR H 107 PHE 0.031 0.001 PHE L 84 TRP 0.017 0.001 TRP R 305 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7281) covalent geometry : angle 0.57917 / 0.29 ( 9951) hydrogen bonds : bond 0.03589 / 2.38 ( 277) hydrogen bonds : angle 4.73633 / 3.46 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7334 (m-10) cc_final: 0.6865 (m-80) REVERT: R 343 TYR cc_start: 0.7360 (t80) cc_final: 0.6942 (t80) REVERT: R 410 GLU cc_start: 0.8251 (tp30) cc_final: 0.7809 (tm-30) REVERT: A 192 MET cc_start: 0.6587 (ttp) cc_final: 0.6367 (ppp) REVERT: H 106 TRP cc_start: 0.5916 (OUTLIER) cc_final: 0.4221 (t-100) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.0720 time to fit residues: 12.1936 Evaluate side-chains 111 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS A 299 ASN B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100976 restraints weight = 13127.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101905 restraints weight = 9347.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102812 restraints weight = 7685.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103542 restraints weight = 6119.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103744 restraints weight = 5739.125| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7281 Z= 0.120 Angle : 0.580 10.353 9951 Z= 0.285 Chirality : 0.041 0.171 1165 Planarity : 0.004 0.045 1244 Dihedral : 5.947 78.215 1039 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 3.71 % Allowed : 18.00 % 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: 0.09 (0.29), residues: 912 helix: 1.79 (0.36), residues: 211 sheet: 0.33 (0.32), residues: 299 loop : -1.09 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 173 TYR 0.023 0.001 TYR B 79 PHE 0.028 0.001 PHE L 84 TRP 0.012 0.001 TRP R 241 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7281) covalent geometry : angle 0.57979 / 0.29 ( 9951) hydrogen bonds : bond 0.03449 / 2.28 ( 277) hydrogen bonds : angle 4.63089 / 3.37 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7339 (m-10) cc_final: 0.6937 (m-80) REVERT: R 343 TYR cc_start: 0.7342 (t80) cc_final: 0.6995 (t80) REVERT: R 410 GLU cc_start: 0.8236 (tp30) cc_final: 0.7820 (tm-30) REVERT: H 106 TRP cc_start: 0.6008 (OUTLIER) cc_final: 0.4299 (t-100) outliers start: 26 outliers final: 16 residues processed: 121 average time/residue: 0.0819 time to fit residues: 13.6066 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 361 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100888 restraints weight = 13213.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101914 restraints weight = 9552.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102867 restraints weight = 7787.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103603 restraints weight = 6088.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103880 restraints weight = 5715.338| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7281 Z= 0.118 Angle : 0.587 11.383 9951 Z= 0.289 Chirality : 0.041 0.171 1165 Planarity : 0.004 0.042 1244 Dihedral : 5.906 76.732 1039 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 2.86 % Allowed : 18.43 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 912 helix: 1.77 (0.36), residues: 211 sheet: 0.32 (0.32), residues: 298 loop : -1.06 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 173 TYR 0.012 0.001 TYR H 107 PHE 0.028 0.001 PHE L 84 TRP 0.012 0.001 TRP R 241 HIS 0.010 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7281) covalent geometry : angle 0.58705 / 0.29 ( 9951) hydrogen bonds : bond 0.03468 / 2.28 ( 277) hydrogen bonds : angle 4.63204 / 3.36 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7326 (m-10) cc_final: 0.6924 (m-80) REVERT: R 295 TRP cc_start: 0.4315 (m-90) cc_final: 0.4071 (m-90) REVERT: R 343 TYR cc_start: 0.7429 (t80) cc_final: 0.7110 (t80) REVERT: R 410 GLU cc_start: 0.8236 (tp30) cc_final: 0.7819 (tm-30) REVERT: A 192 MET cc_start: 0.6423 (ttp) cc_final: 0.5818 (ppp) REVERT: H 106 TRP cc_start: 0.5909 (OUTLIER) cc_final: 0.4234 (t-100) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.0764 time to fit residues: 12.2296 Evaluate side-chains 115 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100689 restraints weight = 13071.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101474 restraints weight = 9247.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103078 restraints weight = 6994.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103303 restraints weight = 5645.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103535 restraints weight = 5521.552| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7281 Z= 0.125 Angle : 0.605 11.729 9951 Z= 0.297 Chirality : 0.042 0.171 1165 Planarity : 0.004 0.054 1244 Dihedral : 5.868 75.170 1039 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 2.57 % Allowed : 19.86 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.29), residues: 912 helix: 1.91 (0.37), residues: 207 sheet: 0.28 (0.32), residues: 299 loop : -1.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 173 TYR 0.026 0.001 TYR B 79 PHE 0.028 0.001 PHE L 84 TRP 0.011 0.001 TRP R 241 HIS 0.011 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7281) covalent geometry : angle 0.60534 / 0.30 ( 9951) hydrogen bonds : bond 0.03482 / 2.30 ( 277) hydrogen bonds : angle 4.56550 / 3.31 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7390 (m-10) cc_final: 0.7024 (m-80) REVERT: R 295 TRP cc_start: 0.4557 (m-90) cc_final: 0.4334 (m-90) REVERT: R 410 GLU cc_start: 0.8240 (tp30) cc_final: 0.7823 (tm-30) REVERT: H 106 TRP cc_start: 0.5959 (OUTLIER) cc_final: 0.4213 (t-100) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.0786 time to fit residues: 12.3911 Evaluate side-chains 113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.0010 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101530 restraints weight = 13147.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102574 restraints weight = 9422.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103536 restraints weight = 7695.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104108 restraints weight = 5983.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104430 restraints weight = 5639.743| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7281 Z= 0.111 Angle : 0.600 11.930 9951 Z= 0.292 Chirality : 0.041 0.174 1165 Planarity : 0.004 0.045 1244 Dihedral : 5.801 73.209 1039 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.92 % Favored : 93.97 % Rotamer: Outliers : 2.71 % Allowed : 19.43 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 912 helix: 1.88 (0.36), residues: 211 sheet: 0.28 (0.32), residues: 298 loop : -1.09 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 173 TYR 0.026 0.001 TYR R 233 PHE 0.030 0.001 PHE L 84 TRP 0.012 0.001 TRP R 241 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7281) covalent geometry : angle 0.60011 / 0.29 ( 9951) hydrogen bonds : bond 0.03345 / 2.20 ( 277) hydrogen bonds : angle 4.51196 / 3.26 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: R 267 TYR cc_start: 0.7434 (m-10) cc_final: 0.6980 (m-80) REVERT: R 295 TRP cc_start: 0.4507 (m-90) cc_final: 0.4253 (m-90) REVERT: R 410 GLU cc_start: 0.8208 (tp30) cc_final: 0.7789 (tm-30) REVERT: A 192 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4917 (ppp) REVERT: A 363 ARG cc_start: 0.7918 (ptt90) cc_final: 0.7684 (ptt90) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.0800 time to fit residues: 12.6790 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102038 restraints weight = 13082.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103296 restraints weight = 8916.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104560 restraints weight = 6666.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104850 restraints weight = 5500.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105022 restraints weight = 5371.284| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7281 Z= 0.112 Angle : 0.605 12.158 9951 Z= 0.294 Chirality : 0.041 0.174 1165 Planarity : 0.004 0.039 1244 Dihedral : 5.735 71.260 1039 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 2.57 % Allowed : 19.86 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.29), residues: 912 helix: 1.86 (0.36), residues: 211 sheet: 0.25 (0.31), residues: 296 loop : -1.08 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 173 TYR 0.026 0.001 TYR B 79 PHE 0.035 0.001 PHE R 320 TRP 0.011 0.001 TRP R 241 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7281) covalent geometry : angle 0.60516 / 0.29 ( 9951) hydrogen bonds : bond 0.03311 / 2.16 ( 277) hydrogen bonds : angle 4.46169 / 3.23 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.29 seconds wall clock time: 21 minutes 57.54 seconds (1317.54 seconds total)