Starting phenix.real_space_refine on Sat Aug 23 06:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.map" model { file = "/net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bw9_44962/08_2025/9bw9_44962.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 54 5.16 5 C 6502 2.51 5 N 1818 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10238 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1897 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 3 Chain: "B" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1958 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 238} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: C, D, G, H Time building chain proxies: 2.42, per 1000 atoms: 0.24 Number of scatterers: 10238 At special positions: 0 Unit cell: (146.28, 129.72, 81.88, 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 54 16.00 O 1864 8.00 N 1818 7.00 C 6502 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: 0.54 Conformation dependent library (CDL) restraints added in 362.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 57.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'G' and resid 348 through 362 removed outlier: 3.675A pdb=" N GLU G 358 " --> pdb=" O ARG G 354 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 381 removed outlier: 3.601A pdb=" N CYS G 373 " --> pdb=" O ASP G 369 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 393 removed outlier: 3.954A pdb=" N HIS G 393 " --> pdb=" O GLN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 404 Processing helix chain 'G' and resid 411 through 424 removed outlier: 3.572A pdb=" N LEU G 419 " --> pdb=" O LYS G 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 363 Processing helix chain 'H' and resid 369 through 383 removed outlier: 4.020A pdb=" N CYS H 373 " --> pdb=" O ASP H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 393 Processing helix chain 'H' and resid 394 through 403 Processing helix chain 'H' and resid 404 through 406 No H-bonds generated for 'chain 'H' and resid 404 through 406' Processing helix chain 'H' and resid 409 through 424 removed outlier: 4.265A pdb=" N MET H 413 " --> pdb=" O SER H 409 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU H 414 " --> pdb=" O GLN H 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS H 424 " --> pdb=" O TYR H 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.945A pdb=" N MET C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.689A pdb=" N GLU C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 4.191A pdb=" N THR C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.931A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 removed outlier: 3.566A pdb=" N LYS C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 222 removed outlier: 3.844A pdb=" N GLN C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 15 removed outlier: 3.755A pdb=" N GLU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.713A pdb=" N ASP D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 26 " --> pdb=" O MET D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 93 through 107 removed outlier: 3.864A pdb=" N GLY D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 133 removed outlier: 3.526A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 167 removed outlier: 4.267A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.628A pdb=" N VAL D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 362 removed outlier: 3.674A pdb=" N GLU E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 381 removed outlier: 3.600A pdb=" N CYS E 373 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 393 removed outlier: 3.954A pdb=" N HIS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 404 Processing helix chain 'E' and resid 411 through 424 removed outlier: 3.571A pdb=" N LEU E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 363 Processing helix chain 'F' and resid 369 through 383 removed outlier: 4.021A pdb=" N CYS F 373 " --> pdb=" O ASP F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 393 Processing helix chain 'F' and resid 394 through 403 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 409 through 424 removed outlier: 4.265A pdb=" N MET F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU F 414 " --> pdb=" O GLN F 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS F 424 " --> pdb=" O TYR F 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.943A pdb=" N MET A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 removed outlier: 3.688A pdb=" N GLU A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 4.190A pdb=" N THR A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.932A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.567A pdb=" N LYS A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 222 removed outlier: 3.844A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.755A pdb=" N GLU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.712A pdb=" N ASP B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 26 " --> pdb=" O MET B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.864A pdb=" N GLY B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.527A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 167 removed outlier: 4.267A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.628A pdb=" N VAL B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 84 through 89 removed outlier: 3.618A pdb=" N GLU C 87 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 74 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 89 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL C 72 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.989A pdb=" N LYS C 240 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 242 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.616A pdb=" N LEU D 74 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS D 114 " --> pdb=" O TRP D 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 63 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL D 113 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 261 removed outlier: 7.081A pdb=" N ALA D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS D 244 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 250 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 252 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 240 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 89 removed outlier: 3.618A pdb=" N GLU A 87 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 74 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 89 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 3.989A pdb=" N LYS A 240 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 242 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 88 removed outlier: 3.616A pdb=" N LEU B 74 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 114 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 63 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL B 113 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 261 removed outlier: 7.080A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS B 244 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 250 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 252 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 240 " --> pdb=" O GLN B 252 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1503 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: 1.23 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.46: 1183 1.46 - 1.57: 5817 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 10408 Sorted by residual: bond pdb=" N ILE A 36 " pdb=" CA ILE A 36 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.59e+00 bond pdb=" N ILE C 36 " pdb=" CA ILE C 36 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.32e+00 bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.18e+00 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.14e-02 7.69e+03 9.00e+00 bond pdb=" N ILE C 251 " pdb=" CA ILE C 251 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.28e-02 6.10e+03 8.88e+00 ... (remaining 10403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 13610 1.67 - 3.34: 337 3.34 - 5.01: 45 5.01 - 6.68: 10 6.68 - 8.35: 2 Bond angle restraints: 14004 Sorted by residual: angle pdb=" O GLY A 237 " pdb=" C GLY A 237 " pdb=" N PRO A 238 " ideal model delta sigma weight residual 121.77 117.31 4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" O GLY C 237 " pdb=" C GLY C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 121.77 117.33 4.44 1.00e+00 1.00e+00 1.98e+01 angle pdb=" CA ILE A 251 " pdb=" C ILE A 251 " pdb=" O ILE A 251 " ideal model delta sigma weight residual 121.72 118.19 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" CA ILE C 251 " pdb=" C ILE C 251 " pdb=" O ILE C 251 " ideal model delta sigma weight residual 121.72 118.21 3.51 9.60e-01 1.09e+00 1.33e+01 angle pdb=" CA ILE A 36 " pdb=" C ILE A 36 " pdb=" O ILE A 36 " ideal model delta sigma weight residual 121.27 117.55 3.72 1.04e+00 9.25e-01 1.28e+01 ... (remaining 13999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5649 17.30 - 34.61: 567 34.61 - 51.91: 104 51.91 - 69.22: 22 69.22 - 86.52: 6 Dihedral angle restraints: 6348 sinusoidal: 2628 harmonic: 3720 Sorted by residual: dihedral pdb=" CA LYS F 407 " pdb=" C LYS F 407 " pdb=" N VAL F 408 " pdb=" CA VAL F 408 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS H 407 " pdb=" C LYS H 407 " pdb=" N VAL H 408 " pdb=" CA VAL H 408 " ideal model delta harmonic sigma weight residual 180.00 164.09 15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB GLU A 92 " pdb=" CG GLU A 92 " pdb=" CD GLU A 92 " pdb=" OE1 GLU A 92 " ideal model delta sinusoidal sigma weight residual 0.00 86.52 -86.52 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 6345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1159 0.043 - 0.085: 313 0.085 - 0.128: 84 0.128 - 0.171: 15 0.171 - 0.213: 13 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA LYS C 240 " pdb=" N LYS C 240 " pdb=" C LYS C 240 " pdb=" CB LYS C 240 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LYS A 240 " pdb=" N LYS A 240 " pdb=" C LYS A 240 " pdb=" CB LYS A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE C 251 " pdb=" N ILE C 251 " pdb=" C ILE C 251 " pdb=" CB ILE C 251 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1581 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 180 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C VAL C 180 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL C 180 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE C 181 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 180 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C VAL A 180 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 180 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 181 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 30 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.33e+00 pdb=" C PRO C 30 " -0.020 2.00e-02 2.50e+03 pdb=" O PRO C 30 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL C 31 " 0.007 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1869 2.77 - 3.30: 10471 3.30 - 3.84: 16453 3.84 - 4.37: 18473 4.37 - 4.90: 30963 Nonbonded interactions: 78229 Sorted by model distance: nonbonded pdb=" O GLY D 118 " pdb=" OG1 THR D 122 " model vdw 2.240 3.040 nonbonded pdb=" O GLY B 118 " pdb=" OG1 THR B 122 " model vdw 2.241 3.040 nonbonded pdb=" O VAL C 150 " pdb=" OG SER C 153 " model vdw 2.265 3.040 nonbonded pdb=" O VAL A 150 " pdb=" OG SER A 153 " model vdw 2.265 3.040 nonbonded pdb=" OE2 GLU A 87 " pdb=" OH TYR B 99 " model vdw 2.271 3.040 ... (remaining 78224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 189 or resid 196 thr \ ough 267)) selection = (chain 'B' and (resid 1 through 41 or resid 56 through 193 or resid 196 through \ 267)) selection = (chain 'C' and (resid 1 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 189 or resid 196 thr \ ough 267)) selection = (chain 'D' and (resid 1 through 41 or resid 56 through 193 or resid 196 through \ 267)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.180 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 0.046 10408 Z= 0.214 Angle : 0.595 8.350 14004 Z= 0.358 Chirality : 0.046 0.213 1584 Planarity : 0.003 0.028 1760 Dihedral : 14.330 86.522 3916 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.44 % Allowed : 0.00 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.88 (0.23), residues: 1242 helix: -0.07 (0.20), residues: 646 sheet: 0.43 (0.43), residues: 152 loop : -1.61 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.012 0.001 TYR A 83 PHE 0.015 0.001 PHE E 423 TRP 0.016 0.002 TRP A 131 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00334 (10408) covalent geometry : angle 0.59507 (14004) hydrogen bonds : bond 0.23900 ( 517) hydrogen bonds : angle 7.49572 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.290 Fit side-chains REVERT: C 9 GLN cc_start: 0.7909 (pp30) cc_final: 0.7257 (pp30) REVERT: A 9 GLN cc_start: 0.7928 (pp30) cc_final: 0.7339 (pp30) REVERT: A 251 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (tp) REVERT: B 154 MET cc_start: 0.7191 (mmt) cc_final: 0.6967 (mmt) outliers start: 16 outliers final: 2 residues processed: 252 average time/residue: 0.0969 time to fit residues: 33.0339 Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN C 171 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 171 HIS ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.200848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150753 restraints weight = 17960.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149364 restraints weight = 16991.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150489 restraints weight = 15471.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152130 restraints weight = 10203.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153308 restraints weight = 8986.201| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10408 Z= 0.156 Angle : 0.580 5.952 14004 Z= 0.312 Chirality : 0.043 0.155 1584 Planarity : 0.004 0.037 1760 Dihedral : 3.921 17.721 1350 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.27 % Allowed : 7.21 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.42 (0.23), residues: 1242 helix: 0.45 (0.20), residues: 658 sheet: 0.46 (0.40), residues: 156 loop : -1.66 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.017 0.001 TYR C 83 PHE 0.009 0.001 PHE G 423 TRP 0.016 0.002 TRP A 131 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00357 (10408) covalent geometry : angle 0.57972 (14004) hydrogen bonds : bond 0.04189 ( 517) hydrogen bonds : angle 4.76147 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 244 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 371 ASN cc_start: 0.8849 (m-40) cc_final: 0.8251 (p0) REVERT: C 9 GLN cc_start: 0.7761 (pp30) cc_final: 0.7366 (pp30) REVERT: C 10 GLU cc_start: 0.8585 (tp30) cc_final: 0.7917 (tp30) REVERT: C 117 ASN cc_start: 0.8329 (m-40) cc_final: 0.7599 (p0) REVERT: C 214 GLN cc_start: 0.6699 (mm-40) cc_final: 0.6304 (tm-30) REVERT: D 242 LEU cc_start: 0.8922 (mm) cc_final: 0.8661 (mm) REVERT: F 371 ASN cc_start: 0.8859 (m-40) cc_final: 0.8254 (p0) REVERT: A 9 GLN cc_start: 0.7727 (pp30) cc_final: 0.7373 (pp30) REVERT: A 10 GLU cc_start: 0.8588 (tp30) cc_final: 0.7893 (tp30) REVERT: A 117 ASN cc_start: 0.8358 (m-40) cc_final: 0.7621 (p0) REVERT: B 242 LEU cc_start: 0.8973 (mm) cc_final: 0.8723 (mm) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.0937 time to fit residues: 32.0651 Evaluate side-chains 203 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 ASN C 95 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN A 95 GLN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.203145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142027 restraints weight = 17901.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140226 restraints weight = 12391.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142219 restraints weight = 9857.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141877 restraints weight = 8709.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142110 restraints weight = 8066.189| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10408 Z= 0.223 Angle : 0.640 6.806 14004 Z= 0.342 Chirality : 0.045 0.149 1584 Planarity : 0.004 0.045 1760 Dihedral : 4.210 16.946 1350 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.36 % Allowed : 4.95 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.41 (0.23), residues: 1242 helix: 0.53 (0.20), residues: 648 sheet: 0.54 (0.41), residues: 156 loop : -1.75 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 20 TYR 0.015 0.002 TYR A 83 PHE 0.016 0.001 PHE A 181 TRP 0.021 0.002 TRP C 131 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00520 (10408) covalent geometry : angle 0.63955 (14004) hydrogen bonds : bond 0.04306 ( 517) hydrogen bonds : angle 4.69902 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5737 (ttt) cc_final: 0.5306 (ttm) REVERT: C 9 GLN cc_start: 0.7723 (pp30) cc_final: 0.7319 (pp30) REVERT: C 10 GLU cc_start: 0.8587 (tp30) cc_final: 0.8051 (tp30) REVERT: C 251 ILE cc_start: 0.7778 (tp) cc_final: 0.7562 (tp) REVERT: D 15 TYR cc_start: 0.7643 (m-10) cc_final: 0.7377 (m-10) REVERT: D 22 MET cc_start: 0.6048 (ppp) cc_final: 0.5812 (ptt) REVERT: D 242 LEU cc_start: 0.9122 (mm) cc_final: 0.8865 (mm) REVERT: F 348 MET cc_start: 0.5681 (ttt) cc_final: 0.5359 (ttm) REVERT: A 11 GLU cc_start: 0.8512 (tp30) cc_final: 0.8123 (tp30) REVERT: B 15 TYR cc_start: 0.7668 (m-10) cc_final: 0.7374 (m-10) REVERT: B 22 MET cc_start: 0.6234 (ptt) cc_final: 0.5491 (ppp) REVERT: B 154 MET cc_start: 0.7367 (mmt) cc_final: 0.7154 (mmt) REVERT: B 242 LEU cc_start: 0.9150 (mm) cc_final: 0.8917 (mm) outliers start: 4 outliers final: 2 residues processed: 234 average time/residue: 0.1057 time to fit residues: 33.6598 Evaluate side-chains 192 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 393 HIS C 117 ASN C 171 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS A 117 ASN A 171 HIS ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.210454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143198 restraints weight = 18627.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.146648 restraints weight = 11916.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149319 restraints weight = 9303.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150434 restraints weight = 8155.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150434 restraints weight = 7622.702| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10408 Z= 0.108 Angle : 0.542 6.520 14004 Z= 0.284 Chirality : 0.042 0.156 1584 Planarity : 0.003 0.032 1760 Dihedral : 3.978 15.882 1350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.18 % Allowed : 2.61 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.15 (0.23), residues: 1242 helix: 0.67 (0.19), residues: 680 sheet: 0.70 (0.41), residues: 156 loop : -1.72 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.009 0.001 TYR C 99 PHE 0.022 0.001 PHE G 423 TRP 0.015 0.002 TRP A 131 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00240 (10408) covalent geometry : angle 0.54207 (14004) hydrogen bonds : bond 0.03193 ( 517) hydrogen bonds : angle 4.32445 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5814 (ttt) cc_final: 0.5329 (ttm) REVERT: C 11 GLU cc_start: 0.8527 (tp30) cc_final: 0.8051 (tp30) REVERT: C 15 TYR cc_start: 0.7665 (m-10) cc_final: 0.7342 (m-10) REVERT: C 117 ASN cc_start: 0.8194 (m-40) cc_final: 0.7499 (p0) REVERT: C 251 ILE cc_start: 0.7765 (tp) cc_final: 0.7540 (tp) REVERT: D 15 TYR cc_start: 0.7618 (m-10) cc_final: 0.7344 (m-10) REVERT: D 242 LEU cc_start: 0.8967 (mm) cc_final: 0.8758 (mm) REVERT: D 266 LYS cc_start: 0.5756 (mtmt) cc_final: 0.5174 (mmtt) REVERT: E 348 MET cc_start: 0.7327 (tpt) cc_final: 0.7111 (tpp) REVERT: F 348 MET cc_start: 0.5797 (ttt) cc_final: 0.5462 (ttm) REVERT: A 10 GLU cc_start: 0.8475 (tp30) cc_final: 0.8248 (tp30) REVERT: A 11 GLU cc_start: 0.8533 (tp30) cc_final: 0.8168 (tp30) REVERT: A 117 ASN cc_start: 0.8194 (m-40) cc_final: 0.7479 (p0) REVERT: B 15 TYR cc_start: 0.7589 (m-10) cc_final: 0.7329 (m-10) REVERT: B 22 MET cc_start: 0.6175 (ptt) cc_final: 0.5655 (ppp) REVERT: B 242 LEU cc_start: 0.9000 (mm) cc_final: 0.8790 (mm) REVERT: B 266 LYS cc_start: 0.5254 (ptpt) cc_final: 0.4667 (mmtt) outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.1026 time to fit residues: 33.9036 Evaluate side-chains 197 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 chunk 91 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 104 optimal weight: 0.0040 chunk 108 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 65 optimal weight: 0.0370 chunk 81 optimal weight: 0.6980 overall best weight: 0.0454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.213595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155413 restraints weight = 18379.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153056 restraints weight = 13153.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154067 restraints weight = 10661.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155008 restraints weight = 8784.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155404 restraints weight = 8064.857| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10408 Z= 0.105 Angle : 0.547 6.614 14004 Z= 0.286 Chirality : 0.042 0.135 1584 Planarity : 0.003 0.031 1760 Dihedral : 3.893 17.282 1350 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.07 (0.23), residues: 1242 helix: 0.72 (0.20), residues: 680 sheet: 0.71 (0.41), residues: 160 loop : -1.63 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 187 TYR 0.004 0.001 TYR A 226 PHE 0.007 0.001 PHE C 181 TRP 0.013 0.002 TRP A 131 HIS 0.004 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00225 (10408) covalent geometry : angle 0.54664 (14004) hydrogen bonds : bond 0.03007 ( 517) hydrogen bonds : angle 4.20989 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5873 (ttt) cc_final: 0.5370 (ttm) REVERT: H 371 ASN cc_start: 0.8914 (m-40) cc_final: 0.8267 (p0) REVERT: C 6 ASP cc_start: 0.7196 (m-30) cc_final: 0.6625 (t70) REVERT: C 10 GLU cc_start: 0.8496 (tp30) cc_final: 0.8200 (tp30) REVERT: C 31 VAL cc_start: 0.8843 (p) cc_final: 0.8620 (m) REVERT: C 96 GLU cc_start: 0.8653 (pp20) cc_final: 0.8367 (pp20) REVERT: C 229 ASP cc_start: 0.6268 (t0) cc_final: 0.6044 (t0) REVERT: D 15 TYR cc_start: 0.7592 (m-10) cc_final: 0.7279 (m-10) REVERT: D 22 MET cc_start: 0.6042 (ptt) cc_final: 0.5458 (ppp) REVERT: D 266 LYS cc_start: 0.5824 (mtmt) cc_final: 0.5209 (mmtt) REVERT: E 348 MET cc_start: 0.7456 (tpt) cc_final: 0.7227 (tpp) REVERT: F 348 MET cc_start: 0.5891 (ttt) cc_final: 0.5488 (ttm) REVERT: F 371 ASN cc_start: 0.8914 (m-40) cc_final: 0.8281 (p0) REVERT: F 395 GLU cc_start: 0.8142 (tp30) cc_final: 0.7939 (tp30) REVERT: A 6 ASP cc_start: 0.7059 (m-30) cc_final: 0.6791 (t70) REVERT: A 9 GLN cc_start: 0.7719 (pp30) cc_final: 0.7305 (pp30) REVERT: A 11 GLU cc_start: 0.8645 (tp30) cc_final: 0.8225 (tp30) REVERT: A 31 VAL cc_start: 0.8809 (p) cc_final: 0.8546 (m) REVERT: A 64 ASP cc_start: 0.7824 (t0) cc_final: 0.7619 (t0) REVERT: A 96 GLU cc_start: 0.8617 (pp20) cc_final: 0.8371 (pp20) REVERT: A 154 MET cc_start: 0.7116 (tpt) cc_final: 0.6829 (tpt) REVERT: A 229 ASP cc_start: 0.6326 (t0) cc_final: 0.6105 (t0) REVERT: B 15 TYR cc_start: 0.7624 (m-10) cc_final: 0.7318 (m-10) REVERT: B 22 MET cc_start: 0.6050 (ptt) cc_final: 0.5501 (ppp) REVERT: B 178 MET cc_start: 0.8926 (ttm) cc_final: 0.8288 (ttm) REVERT: B 266 LYS cc_start: 0.5835 (ptpt) cc_final: 0.5447 (tptp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1022 time to fit residues: 36.5359 Evaluate side-chains 205 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 ASN H 393 HIS C 95 GLN C 117 ASN C 171 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN F 393 HIS A 95 GLN A 117 ASN A 171 HIS ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.212310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.155886 restraints weight = 17990.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154908 restraints weight = 14656.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156563 restraints weight = 10745.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156524 restraints weight = 8438.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156776 restraints weight = 8668.064| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10408 Z= 0.121 Angle : 0.567 6.933 14004 Z= 0.299 Chirality : 0.043 0.155 1584 Planarity : 0.003 0.028 1760 Dihedral : 3.901 16.569 1350 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.18 % Allowed : 2.16 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.02 (0.23), residues: 1242 helix: 0.72 (0.20), residues: 672 sheet: 0.83 (0.42), residues: 160 loop : -1.55 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 187 TYR 0.009 0.001 TYR A 83 PHE 0.016 0.001 PHE G 406 TRP 0.017 0.002 TRP C 131 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00283 (10408) covalent geometry : angle 0.56720 (14004) hydrogen bonds : bond 0.03132 ( 517) hydrogen bonds : angle 4.11660 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5743 (ttt) cc_final: 0.4549 (tmm) REVERT: H 371 ASN cc_start: 0.8839 (m-40) cc_final: 0.8298 (p0) REVERT: H 395 GLU cc_start: 0.8146 (tp30) cc_final: 0.7945 (tp30) REVERT: C 11 GLU cc_start: 0.8646 (tp30) cc_final: 0.8008 (tp30) REVERT: C 15 TYR cc_start: 0.7642 (m-10) cc_final: 0.7386 (m-10) REVERT: C 117 ASN cc_start: 0.8136 (m-40) cc_final: 0.7328 (p0) REVERT: D 15 TYR cc_start: 0.7633 (m-10) cc_final: 0.7373 (m-10) REVERT: D 22 MET cc_start: 0.5986 (ptt) cc_final: 0.5406 (ppp) REVERT: D 178 MET cc_start: 0.9023 (ttm) cc_final: 0.8550 (tpp) REVERT: D 266 LYS cc_start: 0.5894 (mtmt) cc_final: 0.5277 (mmtt) REVERT: E 348 MET cc_start: 0.7416 (tpt) cc_final: 0.7172 (tpp) REVERT: F 348 MET cc_start: 0.5864 (ttt) cc_final: 0.5384 (ttm) REVERT: F 371 ASN cc_start: 0.8772 (m-40) cc_final: 0.8214 (p0) REVERT: A 6 ASP cc_start: 0.7012 (m-30) cc_final: 0.6524 (t70) REVERT: A 9 GLN cc_start: 0.7813 (pp30) cc_final: 0.7607 (pp30) REVERT: A 10 GLU cc_start: 0.8324 (tp30) cc_final: 0.7999 (tp30) REVERT: A 11 GLU cc_start: 0.8611 (tp30) cc_final: 0.8353 (tp30) REVERT: A 96 GLU cc_start: 0.8656 (pp20) cc_final: 0.8403 (pp20) REVERT: A 117 ASN cc_start: 0.8109 (m-40) cc_final: 0.7396 (p0) REVERT: A 229 ASP cc_start: 0.6459 (t0) cc_final: 0.6213 (t0) REVERT: B 15 TYR cc_start: 0.7595 (m-10) cc_final: 0.7276 (m-10) REVERT: B 22 MET cc_start: 0.5859 (ptt) cc_final: 0.5379 (ppp) REVERT: B 266 LYS cc_start: 0.5767 (ptpt) cc_final: 0.5428 (tptp) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.1013 time to fit residues: 35.5903 Evaluate side-chains 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN C 114 HIS C 171 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN A 114 HIS A 171 HIS ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.205170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141447 restraints weight = 17910.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139628 restraints weight = 14818.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141911 restraints weight = 11108.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142562 restraints weight = 9326.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142841 restraints weight = 9056.991| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10408 Z= 0.228 Angle : 0.671 7.560 14004 Z= 0.356 Chirality : 0.046 0.145 1584 Planarity : 0.004 0.031 1760 Dihedral : 4.253 18.391 1350 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.34 (0.23), residues: 1242 helix: 0.56 (0.20), residues: 668 sheet: 0.38 (0.41), residues: 170 loop : -1.77 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 187 TYR 0.017 0.002 TYR C 83 PHE 0.013 0.002 PHE C 185 TRP 0.026 0.003 TRP B 132 HIS 0.008 0.002 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00544 (10408) covalent geometry : angle 0.67103 (14004) hydrogen bonds : bond 0.03841 ( 517) hydrogen bonds : angle 4.44730 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5756 (ttt) cc_final: 0.4680 (tmm) REVERT: H 371 ASN cc_start: 0.8783 (m-40) cc_final: 0.8165 (p0) REVERT: C 11 GLU cc_start: 0.8704 (tp30) cc_final: 0.8157 (tp30) REVERT: C 95 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7376 (mm-40) REVERT: D 15 TYR cc_start: 0.7739 (m-10) cc_final: 0.7498 (m-10) REVERT: D 22 MET cc_start: 0.6303 (ptt) cc_final: 0.5518 (ppp) REVERT: D 266 LYS cc_start: 0.5994 (mtmt) cc_final: 0.5357 (mmtt) REVERT: F 371 ASN cc_start: 0.8765 (m-40) cc_final: 0.8260 (p0) REVERT: A 9 GLN cc_start: 0.7807 (pp30) cc_final: 0.7442 (pp30) REVERT: A 95 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7378 (mm-40) REVERT: B 15 TYR cc_start: 0.7755 (m-10) cc_final: 0.7456 (m-10) REVERT: B 22 MET cc_start: 0.6432 (ptt) cc_final: 0.5551 (ppp) REVERT: B 226 TYR cc_start: 0.5389 (m-10) cc_final: 0.5135 (m-10) REVERT: B 266 LYS cc_start: 0.5944 (ptpt) cc_final: 0.5511 (tptp) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.1138 time to fit residues: 35.9889 Evaluate side-chains 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 ASN C 117 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN A 117 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.208926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151370 restraints weight = 18090.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150159 restraints weight = 13257.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151597 restraints weight = 10465.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151651 restraints weight = 8942.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151873 restraints weight = 8381.993| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10408 Z= 0.129 Angle : 0.614 8.007 14004 Z= 0.321 Chirality : 0.044 0.135 1584 Planarity : 0.003 0.029 1760 Dihedral : 4.132 17.445 1350 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.31 (0.23), residues: 1242 helix: 0.55 (0.20), residues: 678 sheet: 0.37 (0.41), residues: 170 loop : -1.73 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 187 TYR 0.009 0.001 TYR A 83 PHE 0.015 0.001 PHE G 406 TRP 0.020 0.002 TRP B 132 HIS 0.007 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00301 (10408) covalent geometry : angle 0.61391 (14004) hydrogen bonds : bond 0.03249 ( 517) hydrogen bonds : angle 4.28014 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 406 PHE cc_start: 0.8269 (t80) cc_final: 0.7944 (t80) REVERT: H 348 MET cc_start: 0.5824 (ttt) cc_final: 0.5402 (ttm) REVERT: H 371 ASN cc_start: 0.8783 (m-40) cc_final: 0.8166 (p0) REVERT: C 11 GLU cc_start: 0.8697 (tp30) cc_final: 0.8116 (tp30) REVERT: C 117 ASN cc_start: 0.8137 (m-40) cc_final: 0.7313 (p0) REVERT: C 177 GLN cc_start: 0.7380 (pm20) cc_final: 0.7157 (pm20) REVERT: C 258 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7083 (mmtm) REVERT: D 15 TYR cc_start: 0.7675 (m-10) cc_final: 0.7433 (m-10) REVERT: D 22 MET cc_start: 0.6195 (ptt) cc_final: 0.5362 (ppp) REVERT: D 266 LYS cc_start: 0.5806 (mtmt) cc_final: 0.5244 (mmtt) REVERT: F 348 MET cc_start: 0.5965 (ttt) cc_final: 0.5495 (ttm) REVERT: A 9 GLN cc_start: 0.7772 (pp30) cc_final: 0.7483 (pp30) REVERT: A 10 GLU cc_start: 0.8349 (tp30) cc_final: 0.7954 (tp30) REVERT: A 11 GLU cc_start: 0.8647 (tp30) cc_final: 0.8166 (tp30) REVERT: A 87 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 95 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7321 (mm-40) REVERT: A 177 GLN cc_start: 0.7466 (pm20) cc_final: 0.7087 (pm20) REVERT: B 15 TYR cc_start: 0.7671 (m-10) cc_final: 0.7427 (m-10) REVERT: B 22 MET cc_start: 0.6258 (ptt) cc_final: 0.5687 (ptt) REVERT: B 266 LYS cc_start: 0.5816 (ptpt) cc_final: 0.5445 (tptp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1132 time to fit residues: 37.0305 Evaluate side-chains 195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.0670 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 393 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.206523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141552 restraints weight = 18853.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142478 restraints weight = 13987.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142800 restraints weight = 9820.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143074 restraints weight = 9889.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143225 restraints weight = 9401.319| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10408 Z= 0.197 Angle : 0.668 7.763 14004 Z= 0.350 Chirality : 0.045 0.188 1584 Planarity : 0.003 0.032 1760 Dihedral : 4.289 17.743 1350 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.45 (0.23), residues: 1242 helix: 0.45 (0.20), residues: 664 sheet: 0.23 (0.42), residues: 170 loop : -1.71 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 187 TYR 0.016 0.001 TYR C 83 PHE 0.013 0.001 PHE C 26 TRP 0.024 0.002 TRP A 131 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00475 (10408) covalent geometry : angle 0.66803 (14004) hydrogen bonds : bond 0.03646 ( 517) hydrogen bonds : angle 4.41973 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 MET cc_start: 0.5884 (ttt) cc_final: 0.5410 (ttm) REVERT: H 360 LYS cc_start: 0.8895 (tptp) cc_final: 0.8655 (tptp) REVERT: H 371 ASN cc_start: 0.8781 (m-40) cc_final: 0.8215 (p0) REVERT: C 11 GLU cc_start: 0.8751 (tp30) cc_final: 0.8176 (tp30) REVERT: D 15 TYR cc_start: 0.7790 (m-10) cc_final: 0.7581 (m-10) REVERT: D 154 MET cc_start: 0.7364 (mmt) cc_final: 0.6987 (mmt) REVERT: D 178 MET cc_start: 0.9110 (ttm) cc_final: 0.8794 (tpp) REVERT: D 266 LYS cc_start: 0.6007 (mtmt) cc_final: 0.5346 (mmtt) REVERT: F 348 MET cc_start: 0.5971 (ttt) cc_final: 0.5535 (ttm) REVERT: F 360 LYS cc_start: 0.8907 (tptp) cc_final: 0.8654 (tptp) REVERT: F 371 ASN cc_start: 0.8871 (m-40) cc_final: 0.8233 (p0) REVERT: A 9 GLN cc_start: 0.7824 (pp30) cc_final: 0.7538 (pp30) REVERT: A 10 GLU cc_start: 0.8373 (tp30) cc_final: 0.8067 (tp30) REVERT: A 11 GLU cc_start: 0.8744 (tp30) cc_final: 0.8235 (tp30) REVERT: B 15 TYR cc_start: 0.7796 (m-10) cc_final: 0.7561 (m-10) REVERT: B 22 MET cc_start: 0.6632 (ptt) cc_final: 0.6077 (ptt) REVERT: B 154 MET cc_start: 0.7403 (mmt) cc_final: 0.7042 (mmt) REVERT: B 178 MET cc_start: 0.9130 (ttm) cc_final: 0.8828 (tpp) REVERT: B 266 LYS cc_start: 0.5924 (ptpt) cc_final: 0.5445 (tptp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1059 time to fit residues: 32.0838 Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.209751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153119 restraints weight = 17826.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149484 restraints weight = 14266.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150707 restraints weight = 12142.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151542 restraints weight = 10603.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152137 restraints weight = 9374.773| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10408 Z= 0.121 Angle : 0.638 8.422 14004 Z= 0.328 Chirality : 0.044 0.212 1584 Planarity : 0.003 0.030 1760 Dihedral : 4.156 17.143 1350 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.36 (0.23), residues: 1242 helix: 0.49 (0.20), residues: 674 sheet: 0.31 (0.42), residues: 170 loop : -1.65 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.008 0.001 TYR C 99 PHE 0.011 0.001 PHE A 26 TRP 0.020 0.002 TRP B 132 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00281 (10408) covalent geometry : angle 0.63771 (14004) hydrogen bonds : bond 0.03187 ( 517) hydrogen bonds : angle 4.25766 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: H 348 MET cc_start: 0.5969 (ttt) cc_final: 0.5423 (ttm) REVERT: H 371 ASN cc_start: 0.8818 (m-40) cc_final: 0.8246 (p0) REVERT: C 11 GLU cc_start: 0.8707 (tp30) cc_final: 0.8127 (tp30) REVERT: C 177 GLN cc_start: 0.7396 (pm20) cc_final: 0.7157 (pm20) REVERT: D 154 MET cc_start: 0.7224 (mmt) cc_final: 0.6827 (mmt) REVERT: D 178 MET cc_start: 0.9053 (ttm) cc_final: 0.8654 (tpp) REVERT: D 266 LYS cc_start: 0.5784 (mtmt) cc_final: 0.5259 (mmtt) REVERT: F 348 MET cc_start: 0.5990 (ttt) cc_final: 0.5511 (ttm) REVERT: F 371 ASN cc_start: 0.8767 (m-40) cc_final: 0.8222 (p0) REVERT: A 10 GLU cc_start: 0.8335 (tp30) cc_final: 0.7876 (tp30) REVERT: A 11 GLU cc_start: 0.8729 (tp30) cc_final: 0.8197 (tp30) REVERT: A 117 ASN cc_start: 0.8142 (m-40) cc_final: 0.7314 (p0) REVERT: A 177 GLN cc_start: 0.7369 (pm20) cc_final: 0.7030 (pm20) REVERT: B 22 MET cc_start: 0.6301 (ptt) cc_final: 0.5699 (ptt) REVERT: B 154 MET cc_start: 0.7366 (mmt) cc_final: 0.6994 (mmt) REVERT: B 178 MET cc_start: 0.9055 (ttm) cc_final: 0.8674 (tpp) REVERT: B 266 LYS cc_start: 0.5773 (ptpt) cc_final: 0.5304 (tptp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1048 time to fit residues: 33.2762 Evaluate side-chains 190 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 ASN H 393 HIS C 95 GLN C 117 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN A 95 GLN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.207558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146012 restraints weight = 18219.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147411 restraints weight = 12820.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146694 restraints weight = 9282.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146706 restraints weight = 9497.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146825 restraints weight = 9663.795| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10408 Z= 0.145 Angle : 0.642 7.847 14004 Z= 0.332 Chirality : 0.044 0.177 1584 Planarity : 0.003 0.028 1760 Dihedral : 4.170 17.196 1350 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.18 % Allowed : 0.09 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.36 (0.23), residues: 1242 helix: 0.49 (0.20), residues: 674 sheet: 0.29 (0.41), residues: 170 loop : -1.66 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 187 TYR 0.009 0.001 TYR C 83 PHE 0.012 0.001 PHE G 406 TRP 0.022 0.002 TRP B 132 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00349 (10408) covalent geometry : angle 0.64150 (14004) hydrogen bonds : bond 0.03321 ( 517) hydrogen bonds : angle 4.24091 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.97 seconds wall clock time: 31 minutes 55.65 seconds (1915.65 seconds total)