Starting phenix.real_space_refine on Thu Sep 18 03:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.map" model { file = "/net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iso_60840/09_2025/9iso_60840.cif" } resolution = 2.81 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= -0.002 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8338 2.51 5 N 2226 2.21 5 O 2504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13130 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4620 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 562} Chain: "B" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4620 Classifications: {'peptide': 595} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 562} Chain: "C" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1921 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain: "D" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1921 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PQQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PQQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.28 Number of scatterers: 13130 At special positions: 0 Unit cell: (97.01, 107.69, 126.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2504 8.00 N 2226 7.00 C 8338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 104 " distance=2.04 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 104 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 415 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 76 " 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: 1.04 Conformation dependent library (CDL) restraints added in 644.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 26 sheets defined 19.4% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.602A pdb=" N SER A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.572A pdb=" N ALA A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.708A pdb=" N THR A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.519A pdb=" N LEU A 556 " --> pdb=" O THR A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 563 through 566 removed outlier: 4.208A pdb=" N ALA A 566 " --> pdb=" O LYS A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.648A pdb=" N ALA B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.831A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.611A pdb=" N MET B 269 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.568A pdb=" N GLY B 375 " --> pdb=" O PRO B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.607A pdb=" N ALA B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 568 removed outlier: 3.692A pdb=" N ASN B 567 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.730A pdb=" N ALA C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.002A pdb=" N VAL C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 188 through 197 removed outlier: 5.277A pdb=" N ARG C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 removed outlier: 3.850A pdb=" N GLU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.792A pdb=" N ILE C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 132 through 142 removed outlier: 3.529A pdb=" N ALA D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.154A pdb=" N VAL D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.566A pdb=" N MET D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 247 through 259 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 47 removed outlier: 6.855A pdb=" N VAL A 577 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR A 45 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 575 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 580 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLN A 529 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.883A pdb=" N THR A 75 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN A 89 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA A 77 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.777A pdb=" N ASN A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 145 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 137 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR A 143 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.545A pdb=" N TYR A 163 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 184 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 197 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 186 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.271A pdb=" N ILE A 280 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 293 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 282 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.542A pdb=" N SER A 347 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP A 339 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 345 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 361 removed outlier: 3.915A pdb=" N SER A 360 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 382 through 385 removed outlier: 5.669A pdb=" N LYS A 383 " --> pdb=" O TRP A 418 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP A 418 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.799A pdb=" N GLY A 453 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP A 467 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 481 removed outlier: 3.757A pdb=" N VAL A 487 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 40 through 47 removed outlier: 6.863A pdb=" N VAL B 577 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 45 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 575 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 580 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLN B 529 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.242A pdb=" N TRP B 88 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY B 79 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 86 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.054A pdb=" N TRP B 145 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN B 137 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 143 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.599A pdb=" N TYR B 163 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP B 196 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP B 188 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 194 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 247 through 249 removed outlier: 6.505A pdb=" N ASP B 284 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 290 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.636A pdb=" N SER B 347 " --> pdb=" O THR B 337 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP B 339 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 345 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 358 through 361 removed outlier: 4.007A pdb=" N SER B 360 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 382 through 385 removed outlier: 3.546A pdb=" N ASP B 384 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET B 416 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 399 through 401 removed outlier: 3.597A pdb=" N LEU B 406 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 453 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP B 467 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 479 through 481 removed outlier: 3.535A pdb=" N VAL B 487 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AC4, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AC5, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.671A pdb=" N VAL C 127 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N PHE C 187 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.671A pdb=" N VAL C 127 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N PHE C 187 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 96 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 53 through 59 removed outlier: 6.332A pdb=" N LEU D 20 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL D 57 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 22 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU D 59 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 24 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE D 80 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 11.301A pdb=" N ALA D 25 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 12.516A pdb=" N LEU D 82 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 80 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY D 228 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR D 96 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 127 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N PHE D 187 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.702A pdb=" N TYR D 96 " --> pdb=" O GLN D 225 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1017 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: 2.24 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4272 1.34 - 1.46: 3211 1.46 - 1.59: 5869 1.59 - 1.72: 0 1.72 - 1.84: 112 Bond restraints: 13464 Sorted by residual: bond pdb=" CA ASN A 73 " pdb=" C ASN A 73 " ideal model delta sigma weight residual 1.528 1.501 0.027 1.25e-02 6.40e+03 4.84e+00 bond pdb=" N PHE A 71 " pdb=" CA PHE A 71 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.04e-02 9.25e+03 4.49e+00 bond pdb=" C3A PQQ B 701 " pdb=" C4 PQQ B 701 " ideal model delta sigma weight residual 1.426 1.459 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C ASN A 73 " pdb=" O ASN A 73 " ideal model delta sigma weight residual 1.233 1.211 0.021 1.30e-02 5.92e+03 2.70e+00 bond pdb=" N SER A 70 " pdb=" CA SER A 70 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.62e+00 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17872 1.87 - 3.73: 360 3.73 - 5.60: 39 5.60 - 7.46: 9 7.46 - 9.33: 2 Bond angle restraints: 18282 Sorted by residual: angle pdb=" C PHE A 71 " pdb=" N PRO A 72 " pdb=" CA PRO A 72 " ideal model delta sigma weight residual 119.87 114.09 5.78 1.04e+00 9.25e-01 3.09e+01 angle pdb=" N PHE A 71 " pdb=" CA PHE A 71 " pdb=" C PHE A 71 " ideal model delta sigma weight residual 113.16 120.41 -7.25 1.42e+00 4.96e-01 2.61e+01 angle pdb=" N MET B 378 " pdb=" CA MET B 378 " pdb=" C MET B 378 " ideal model delta sigma weight residual 113.28 107.68 5.60 1.22e+00 6.72e-01 2.11e+01 angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 113.39 108.26 5.13 1.47e+00 4.63e-01 1.22e+01 angle pdb=" C PHE A 71 " pdb=" CA PHE A 71 " pdb=" CB PHE A 71 " ideal model delta sigma weight residual 112.05 106.56 5.49 1.91e+00 2.74e-01 8.25e+00 ... (remaining 18277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7092 15.63 - 31.27: 651 31.27 - 46.90: 148 46.90 - 62.53: 24 62.53 - 78.17: 12 Dihedral angle restraints: 7927 sinusoidal: 3159 harmonic: 4768 Sorted by residual: dihedral pdb=" CA CYS B 103 " pdb=" C CYS B 103 " pdb=" N CYS B 104 " pdb=" CA CYS B 104 " ideal model delta harmonic sigma weight residual -180.00 -151.54 -28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 415 " pdb=" CB CYS B 415 " ideal model delta sinusoidal sigma weight residual 93.00 51.33 41.67 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA CYS A 103 " pdb=" C CYS A 103 " pdb=" N CYS A 104 " pdb=" CA CYS A 104 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 7924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1633 0.061 - 0.123: 273 0.123 - 0.184: 11 0.184 - 0.245: 2 0.245 - 0.307: 1 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA PHE A 71 " pdb=" N PHE A 71 " pdb=" C PHE A 71 " pdb=" CB PHE A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ASP B 379 " pdb=" N ASP B 379 " pdb=" C ASP B 379 " pdb=" CB ASP B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN A 73 " pdb=" N ASN A 73 " pdb=" C ASN A 73 " pdb=" CB ASN A 73 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 1917 not shown) Planarity restraints: 2384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A PQQ A 701 " -0.018 2.00e-02 2.50e+03 9.89e-02 4.40e+02 pdb=" C2 PQQ A 701 " -0.046 2.00e-02 2.50e+03 pdb=" C2X PQQ A 701 " -0.086 2.00e-02 2.50e+03 pdb=" C3 PQQ A 701 " 0.014 2.00e-02 2.50e+03 pdb=" C3A PQQ A 701 " 0.034 2.00e-02 2.50e+03 pdb=" C4 PQQ A 701 " 0.092 2.00e-02 2.50e+03 pdb=" C5 PQQ A 701 " -0.083 2.00e-02 2.50e+03 pdb=" C6A PQQ A 701 " -0.042 2.00e-02 2.50e+03 pdb=" C7 PQQ A 701 " 0.015 2.00e-02 2.50e+03 pdb=" C7X PQQ A 701 " 0.028 2.00e-02 2.50e+03 pdb=" C8 PQQ A 701 " 0.049 2.00e-02 2.50e+03 pdb=" C9 PQQ A 701 " 0.038 2.00e-02 2.50e+03 pdb=" C9A PQQ A 701 " -0.009 2.00e-02 2.50e+03 pdb=" C9X PQQ A 701 " 0.079 2.00e-02 2.50e+03 pdb=" N1 PQQ A 701 " -0.064 2.00e-02 2.50e+03 pdb=" N6 PQQ A 701 " -0.028 2.00e-02 2.50e+03 pdb=" O4 PQQ A 701 " 0.270 2.00e-02 2.50e+03 pdb=" O5 PQQ A 701 " -0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 69 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C THR A 69 " -0.052 2.00e-02 2.50e+03 pdb=" O THR A 69 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 70 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A PQQ B 701 " 0.010 2.00e-02 2.50e+03 1.01e-02 4.63e+00 pdb=" C2 PQQ B 701 " -0.009 2.00e-02 2.50e+03 pdb=" C2X PQQ B 701 " -0.020 2.00e-02 2.50e+03 pdb=" C3 PQQ B 701 " -0.007 2.00e-02 2.50e+03 pdb=" C3A PQQ B 701 " 0.003 2.00e-02 2.50e+03 pdb=" C4 PQQ B 701 " 0.007 2.00e-02 2.50e+03 pdb=" C5 PQQ B 701 " -0.001 2.00e-02 2.50e+03 pdb=" C6A PQQ B 701 " 0.000 2.00e-02 2.50e+03 pdb=" C7 PQQ B 701 " -0.007 2.00e-02 2.50e+03 pdb=" C7X PQQ B 701 " -0.016 2.00e-02 2.50e+03 pdb=" C8 PQQ B 701 " 0.001 2.00e-02 2.50e+03 pdb=" C9 PQQ B 701 " 0.010 2.00e-02 2.50e+03 pdb=" C9A PQQ B 701 " 0.013 2.00e-02 2.50e+03 pdb=" C9X PQQ B 701 " 0.018 2.00e-02 2.50e+03 pdb=" N1 PQQ B 701 " -0.001 2.00e-02 2.50e+03 pdb=" N6 PQQ B 701 " -0.007 2.00e-02 2.50e+03 pdb=" O4 PQQ B 701 " 0.014 2.00e-02 2.50e+03 pdb=" O5 PQQ B 701 " -0.006 2.00e-02 2.50e+03 ... (remaining 2381 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 205 2.68 - 3.23: 11618 3.23 - 3.79: 18330 3.79 - 4.34: 26037 4.34 - 4.90: 44404 Nonbonded interactions: 100594 Sorted by model distance: nonbonded pdb=" O GLU C 245 " pdb=" NZ LYS C 248 " model vdw 2.125 3.120 nonbonded pdb=" N1 PQQ A 701 " pdb=" O9A PQQ A 701 " model vdw 2.172 3.120 nonbonded pdb=" NE2 GLN A 94 " pdb=" OD2 ASP A 130 " model vdw 2.180 3.120 nonbonded pdb=" O ASP B 379 " pdb=" OD1 ASP B 379 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP A 500 " pdb=" OG1 THR A 503 " model vdw 2.185 3.040 ... (remaining 100589 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.003 0.062 13469 Z= 0.147 Angle : 0.616 9.329 18292 Z= 0.325 Chirality : 0.045 0.307 1920 Planarity : 0.005 0.099 2384 Dihedral : 12.836 78.168 4908 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -1.10 (0.19), residues: 1680 helix: 0.46 (0.36), residues: 222 sheet: -0.11 (0.25), residues: 408 loop : -1.29 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 499 TYR 0.015 0.001 TYR A 163 PHE 0.017 0.002 PHE C 187 TRP 0.021 0.001 TRP B 114 HIS 0.008 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00324 (13464) covalent geometry : angle 0.61427 (18282) SS BOND : bond 0.00943 ( 5) SS BOND : angle 2.19451 ( 10) hydrogen bonds : bond 0.17438 ( 384) hydrogen bonds : angle 6.41266 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 80 ILE cc_start: 0.8971 (tp) cc_final: 0.8130 (tp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.7400 time to fit residues: 129.9506 Evaluate side-chains 92 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 295 GLN B 128 GLN C 225 GLN D 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051862 restraints weight = 38208.900| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.39 r_work: 0.2779 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13469 Z= 0.168 Angle : 0.603 5.806 18292 Z= 0.316 Chirality : 0.045 0.239 1920 Planarity : 0.004 0.052 2384 Dihedral : 5.081 71.387 1838 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.47 % Allowed : 9.38 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -1.06 (0.19), residues: 1680 helix: 0.33 (0.34), residues: 234 sheet: -0.05 (0.25), residues: 408 loop : -1.26 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.012 0.001 TYR D 95 PHE 0.025 0.002 PHE B 46 TRP 0.015 0.001 TRP B 88 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00401 (13464) covalent geometry : angle 0.60163 (18282) SS BOND : bond 0.00953 ( 5) SS BOND : angle 1.95884 ( 10) hydrogen bonds : bond 0.04559 ( 384) hydrogen bonds : angle 5.05819 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 438 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8356 (mtm) REVERT: B 426 ARG cc_start: 0.8803 (mmm-85) cc_final: 0.8440 (mtp180) REVERT: D 27 GLN cc_start: 0.8702 (tt0) cc_final: 0.8491 (mt0) REVERT: D 39 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8975 (tp30) REVERT: D 55 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 163 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8349 (mp10) outliers start: 20 outliers final: 3 residues processed: 100 average time/residue: 0.7013 time to fit residues: 75.6858 Evaluate side-chains 80 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain D residue 39 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 0.0060 chunk 126 optimal weight: 6.9990 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052646 restraints weight = 38891.174| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.50 r_work: 0.2808 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13469 Z= 0.110 Angle : 0.534 6.376 18292 Z= 0.279 Chirality : 0.043 0.194 1920 Planarity : 0.004 0.050 2384 Dihedral : 4.870 76.684 1838 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.39 % Allowed : 10.78 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.98 (0.19), residues: 1680 helix: 0.41 (0.35), residues: 236 sheet: 0.00 (0.26), residues: 380 loop : -1.18 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.011 0.001 TYR D 95 PHE 0.017 0.001 PHE A 430 TRP 0.011 0.001 TRP B 88 HIS 0.002 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00257 (13464) covalent geometry : angle 0.53144 (18282) SS BOND : bond 0.00930 ( 5) SS BOND : angle 2.49031 ( 10) hydrogen bonds : bond 0.03701 ( 384) hydrogen bonds : angle 4.86340 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.522 Fit side-chains REVERT: A 438 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8332 (mtm) REVERT: B 119 LYS cc_start: 0.8768 (mppt) cc_final: 0.8523 (mppt) REVERT: C 227 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8569 (tpt) REVERT: D 39 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9006 (tp30) outliers start: 19 outliers final: 5 residues processed: 92 average time/residue: 0.6181 time to fit residues: 62.0957 Evaluate side-chains 85 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN D 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050630 restraints weight = 39414.814| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.44 r_work: 0.2740 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13469 Z= 0.190 Angle : 0.582 6.411 18292 Z= 0.307 Chirality : 0.045 0.187 1920 Planarity : 0.004 0.052 2384 Dihedral : 5.071 76.200 1838 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.13 % Allowed : 11.51 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -1.05 (0.19), residues: 1680 helix: 0.51 (0.35), residues: 236 sheet: -0.09 (0.25), residues: 396 loop : -1.27 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.012 0.001 TYR A 163 PHE 0.018 0.002 PHE A 430 TRP 0.011 0.001 TRP B 88 HIS 0.003 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00452 (13464) covalent geometry : angle 0.57979 (18282) SS BOND : bond 0.00919 ( 5) SS BOND : angle 2.14094 ( 10) hydrogen bonds : bond 0.04725 ( 384) hydrogen bonds : angle 4.92388 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.536 Fit side-chains REVERT: A 378 MET cc_start: 0.7128 (mmm) cc_final: 0.6820 (tmm) REVERT: C 225 GLN cc_start: 0.8287 (mm110) cc_final: 0.7641 (mm-40) REVERT: C 227 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8510 (tpt) outliers start: 29 outliers final: 9 residues processed: 92 average time/residue: 0.6219 time to fit residues: 62.6352 Evaluate side-chains 82 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 106 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 117 optimal weight: 0.0050 chunk 158 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN D 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049510 restraints weight = 39204.844| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.47 r_work: 0.2718 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13469 Z= 0.169 Angle : 0.566 6.661 18292 Z= 0.299 Chirality : 0.044 0.185 1920 Planarity : 0.004 0.053 2384 Dihedral : 5.051 77.811 1838 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.61 % Allowed : 13.05 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -1.01 (0.20), residues: 1680 helix: 0.59 (0.35), residues: 236 sheet: -0.12 (0.24), residues: 422 loop : -1.25 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.011 0.001 TYR B 535 PHE 0.016 0.001 PHE A 430 TRP 0.012 0.001 TRP B 88 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00405 (13464) covalent geometry : angle 0.56392 (18282) SS BOND : bond 0.01018 ( 5) SS BOND : angle 2.14858 ( 10) hydrogen bonds : bond 0.04434 ( 384) hydrogen bonds : angle 4.89617 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.559 Fit side-chains REVERT: A 321 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (ptmt) REVERT: A 378 MET cc_start: 0.7215 (mmm) cc_final: 0.6773 (tmm) REVERT: C 227 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8530 (tpt) REVERT: D 39 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8469 (mm-30) outliers start: 22 outliers final: 10 residues processed: 90 average time/residue: 0.6591 time to fit residues: 64.7459 Evaluate side-chains 86 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050606 restraints weight = 38672.295| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.46 r_work: 0.2757 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13469 Z= 0.107 Angle : 0.518 7.122 18292 Z= 0.273 Chirality : 0.043 0.186 1920 Planarity : 0.004 0.052 2384 Dihedral : 4.807 81.042 1838 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.10 % Allowed : 14.37 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.85 (0.20), residues: 1680 helix: 0.68 (0.35), residues: 236 sheet: -0.07 (0.24), residues: 450 loop : -1.13 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.011 0.001 TYR A 535 PHE 0.014 0.001 PHE A 430 TRP 0.011 0.001 TRP B 88 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00255 (13464) covalent geometry : angle 0.51659 (18282) SS BOND : bond 0.00957 ( 5) SS BOND : angle 1.95305 ( 10) hydrogen bonds : bond 0.03548 ( 384) hydrogen bonds : angle 4.77673 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.536 Fit side-chains REVERT: A 378 MET cc_start: 0.7199 (mmm) cc_final: 0.6992 (tmm) REVERT: D 39 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: D 252 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8754 (mt-10) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.6528 time to fit residues: 62.2280 Evaluate side-chains 81 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049540 restraints weight = 38837.926| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.41 r_work: 0.2720 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13469 Z= 0.165 Angle : 0.564 10.492 18292 Z= 0.296 Chirality : 0.044 0.186 1920 Planarity : 0.004 0.053 2384 Dihedral : 4.962 78.327 1838 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.47 % Allowed : 14.52 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.96 (0.20), residues: 1680 helix: 0.78 (0.35), residues: 234 sheet: -0.08 (0.24), residues: 418 loop : -1.25 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.011 0.001 TYR B 535 PHE 0.014 0.001 PHE A 430 TRP 0.010 0.001 TRP B 88 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00396 (13464) covalent geometry : angle 0.56207 (18282) SS BOND : bond 0.00948 ( 5) SS BOND : angle 2.02641 ( 10) hydrogen bonds : bond 0.04378 ( 384) hydrogen bonds : angle 4.84992 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.546 Fit side-chains REVERT: A 321 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7695 (ptmt) REVERT: D 39 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8977 (tp30) outliers start: 20 outliers final: 10 residues processed: 91 average time/residue: 0.6853 time to fit residues: 68.0012 Evaluate side-chains 85 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 66 optimal weight: 0.0070 chunk 163 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050289 restraints weight = 38806.558| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.46 r_work: 0.2745 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13469 Z= 0.119 Angle : 0.529 9.023 18292 Z= 0.277 Chirality : 0.043 0.195 1920 Planarity : 0.004 0.053 2384 Dihedral : 4.832 80.475 1838 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.17 % Allowed : 15.18 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.85 (0.20), residues: 1680 helix: 0.86 (0.36), residues: 234 sheet: -0.05 (0.24), residues: 430 loop : -1.16 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.011 0.001 TYR A 535 PHE 0.012 0.001 PHE A 430 TRP 0.011 0.001 TRP B 88 HIS 0.003 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00284 (13464) covalent geometry : angle 0.52733 (18282) SS BOND : bond 0.00934 ( 5) SS BOND : angle 1.90268 ( 10) hydrogen bonds : bond 0.03677 ( 384) hydrogen bonds : angle 4.76403 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.544 Fit side-chains REVERT: A 310 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8621 (mmm) REVERT: A 321 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7670 (ptmt) REVERT: A 378 MET cc_start: 0.7248 (mmm) cc_final: 0.6680 (tmm) REVERT: B 378 MET cc_start: 0.7937 (ttm) cc_final: 0.7688 (ttm) REVERT: D 32 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6147 (mpt) REVERT: D 39 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8964 (tp30) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.6854 time to fit residues: 65.8905 Evaluate side-chains 86 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 9 optimal weight: 0.0370 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050300 restraints weight = 39285.780| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.47 r_work: 0.2740 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13469 Z= 0.124 Angle : 0.541 11.791 18292 Z= 0.282 Chirality : 0.043 0.190 1920 Planarity : 0.004 0.053 2384 Dihedral : 4.824 80.738 1838 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.17 % Allowed : 15.40 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.86 (0.20), residues: 1680 helix: 0.72 (0.35), residues: 234 sheet: -0.05 (0.24), residues: 430 loop : -1.14 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.011 0.001 TYR A 535 PHE 0.012 0.001 PHE A 430 TRP 0.010 0.001 TRP B 88 HIS 0.003 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00299 (13464) covalent geometry : angle 0.53897 (18282) SS BOND : bond 0.00941 ( 5) SS BOND : angle 1.92433 ( 10) hydrogen bonds : bond 0.03771 ( 384) hydrogen bonds : angle 4.82380 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.559 Fit side-chains REVERT: A 310 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8617 (mmm) REVERT: A 321 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7711 (ptmt) REVERT: B 378 MET cc_start: 0.7933 (ttm) cc_final: 0.7690 (ttm) REVERT: D 27 GLN cc_start: 0.8198 (mt0) cc_final: 0.7991 (mt0) REVERT: D 32 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6152 (mpt) REVERT: D 39 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8973 (tp30) REVERT: D 252 GLU cc_start: 0.8094 (mp0) cc_final: 0.7826 (mp0) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.6951 time to fit residues: 65.9267 Evaluate side-chains 86 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 89 optimal weight: 4.9990 chunk 62 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051265 restraints weight = 38942.227| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.48 r_work: 0.2776 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13469 Z= 0.100 Angle : 0.510 10.188 18292 Z= 0.267 Chirality : 0.042 0.200 1920 Planarity : 0.004 0.053 2384 Dihedral : 4.677 83.774 1838 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.10 % Allowed : 15.25 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.74 (0.20), residues: 1680 helix: 0.72 (0.36), residues: 234 sheet: -0.05 (0.24), residues: 450 loop : -1.01 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.015 0.001 TYR D 65 PHE 0.010 0.001 PHE A 430 TRP 0.011 0.001 TRP B 88 HIS 0.005 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00240 (13464) covalent geometry : angle 0.50839 (18282) SS BOND : bond 0.00934 ( 5) SS BOND : angle 1.87156 ( 10) hydrogen bonds : bond 0.03277 ( 384) hydrogen bonds : angle 4.74369 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.583 Fit side-chains REVERT: A 321 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7682 (ptmt) REVERT: B 364 LYS cc_start: 0.9100 (mppt) cc_final: 0.8879 (mppt) REVERT: D 32 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6220 (mpt) REVERT: D 39 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8956 (tp30) REVERT: D 252 GLU cc_start: 0.8130 (mp0) cc_final: 0.7880 (mp0) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.6823 time to fit residues: 64.8452 Evaluate side-chains 85 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 159 optimal weight: 0.0060 chunk 58 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 chunk 165 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.070310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052271 restraints weight = 38662.033| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.48 r_work: 0.2786 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13469 Z= 0.092 Angle : 0.510 12.769 18292 Z= 0.264 Chirality : 0.042 0.207 1920 Planarity : 0.004 0.053 2384 Dihedral : 4.586 85.912 1838 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.95 % Allowed : 15.32 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 aren not related in a simple way. whole: -0.66 (0.20), residues: 1680 helix: 0.78 (0.36), residues: 234 sheet: -0.02 (0.24), residues: 450 loop : -0.95 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.018 0.001 TYR D 65 PHE 0.011 0.001 PHE A 430 TRP 0.010 0.001 TRP B 88 HIS 0.005 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00219 (13464) covalent geometry : angle 0.50872 (18282) SS BOND : bond 0.00930 ( 5) SS BOND : angle 1.85006 ( 10) hydrogen bonds : bond 0.03034 ( 384) hydrogen bonds : angle 4.64671 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.27 seconds wall clock time: 69 minutes 45.07 seconds (4185.07 seconds total)