Starting phenix.real_space_refine on Thu Jul 2 14:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4x_17429/07_2026/8p4x_17429.cif" } resolution = 2.57 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= -0.001 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 5564 2.51 5 N 1456 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Restraints were copied for chains: B Time building chain proxies: 2.57, per 1000 atoms: 0.29 Number of scatterers: 8756 At special positions: 0 Unit cell: (95.682, 104.302, 95.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 4 15.00 Mg 2 11.99 O 1652 8.00 N 1456 7.00 C 5564 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: 0.51 Conformation dependent library (CDL) restraints added in 205.0 milliseconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 56.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 77 through 99 removed outlier: 3.626A pdb=" N LYS A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.762A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.710A pdb=" N GLU A 234 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.880A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.555A pdb=" N CYS A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.845A pdb=" N GLY A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS A 442 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.614A pdb=" N TYR A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 505 through 524 removed outlier: 3.588A pdb=" N SER A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.536A pdb=" N VAL A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 77 through 99 removed outlier: 3.627A pdb=" N LYS B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP B 139 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.763A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.709A pdb=" N GLU B 234 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU B 317 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 318' Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.881A pdb=" N TRP B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 330 " --> pdb=" O TYR B 326 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.556A pdb=" N CYS B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.844A pdb=" N GLY B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA B 425 " --> pdb=" O TRP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS B 442 " --> pdb=" O CYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.615A pdb=" N TYR B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 505 through 524 removed outlier: 3.587A pdb=" N SER B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.537A pdb=" N VAL B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.299A pdb=" N VAL A 33 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR A 126 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 35 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU A 128 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N TRP A 37 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.300A pdb=" N VAL B 33 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 126 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 35 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU B 128 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP B 37 " --> pdb=" O GLU B 128 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2744 1.34 - 1.46: 2088 1.46 - 1.58: 4014 1.58 - 1.69: 4 1.69 - 1.81: 114 Bond restraints: 8964 Sorted by residual: bond pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5' FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5B FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.49e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11902 1.48 - 2.96: 221 2.96 - 4.44: 60 4.44 - 5.93: 5 5.93 - 7.41: 6 Bond angle restraints: 12194 Sorted by residual: angle pdb=" O1P FAD B 601 " pdb=" P FAD B 601 " pdb=" O2P FAD B 601 " ideal model delta sigma weight residual 122.50 115.09 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" O1P FAD A 601 " pdb=" P FAD A 601 " pdb=" O2P FAD A 601 " ideal model delta sigma weight residual 122.50 115.10 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O5B FAD B 601 " ideal model delta sigma weight residual 104.10 111.17 -7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O5B FAD A 601 " ideal model delta sigma weight residual 104.10 111.16 -7.06 3.00e+00 1.11e-01 5.54e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O2A FAD B 601 " ideal model delta sigma weight residual 121.20 114.74 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 12189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 4980 18.12 - 36.25: 188 36.25 - 54.37: 50 54.37 - 72.50: 8 72.50 - 90.62: 6 Dihedral angle restraints: 5232 sinusoidal: 2184 harmonic: 3048 Sorted by residual: dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 39 " pdb=" C ARG A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 -152.39 90.62 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 5229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 662 0.025 - 0.049: 346 0.049 - 0.074: 114 0.074 - 0.098: 42 0.098 - 0.123: 56 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL B 33 " pdb=" N VAL B 33 " pdb=" C VAL B 33 " pdb=" CB VAL B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" C2B FAD A 601 " pdb=" C1B FAD A 601 " pdb=" C3B FAD A 601 " pdb=" O2B FAD A 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1217 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 526 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 526 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 533 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 534 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.017 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.23: 7683 3.23 - 3.78: 12540 3.78 - 4.34: 18624 4.34 - 4.90: 30825 Nonbonded interactions: 69792 Sorted by model distance: nonbonded pdb=" O HOH B 717 " pdb=" O HOH B 740 " model vdw 2.112 3.040 nonbonded pdb=" O HOH A 717 " pdb=" O HOH A 740 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP B 420 " pdb=" O HOH B 701 " model vdw 2.116 3.040 nonbonded pdb=" OD2 ASP A 420 " pdb=" O HOH A 701 " model vdw 2.116 3.040 nonbonded pdb=" NH1 ARG A 324 " pdb=" O HOH A 701 " model vdw 2.125 3.120 ... (remaining 69787 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8964 Z= 0.183 Angle : 0.561 7.407 12194 Z= 0.284 Chirality : 0.040 0.123 1220 Planarity : 0.004 0.040 1552 Dihedral : 11.134 90.621 3276 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1048 helix: 0.99 (0.24), residues: 528 sheet: 0.00 (0.58), residues: 70 loop : -1.38 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.012 0.001 TYR B 326 PHE 0.012 0.001 PHE B 543 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8964) covalent geometry : angle 0.56066 / 0.28 (12194) hydrogen bonds : bond 0.18388 / 12.97 ( 340) hydrogen bonds : angle 5.20894 / 3.79 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.351 Fit side-chains REVERT: A 115 GLN cc_start: 0.7079 (tt0) cc_final: 0.6857 (tt0) REVERT: A 200 ASP cc_start: 0.7123 (t70) cc_final: 0.6896 (t0) REVERT: B 115 GLN cc_start: 0.7076 (tt0) cc_final: 0.6854 (tt0) REVERT: B 200 ASP cc_start: 0.7121 (t70) cc_final: 0.6893 (t0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4938 time to fit residues: 76.1863 Evaluate side-chains 127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113855 restraints weight = 8084.962| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.15 r_work: 0.3019 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8964 Z= 0.209 Angle : 0.698 8.106 12194 Z= 0.359 Chirality : 0.049 0.141 1220 Planarity : 0.006 0.046 1552 Dihedral : 6.034 82.080 1146 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 8.42 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1048 helix: 0.83 (0.23), residues: 542 sheet: 0.50 (0.59), residues: 66 loop : -1.35 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 515 TYR 0.011 0.002 TYR A 465 PHE 0.018 0.003 PHE B 543 TRP 0.020 0.002 TRP A 430 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 ( 8964) covalent geometry : angle 0.69849 / 0.36 (12194) hydrogen bonds : bond 0.08778 / 5.88 ( 340) hydrogen bonds : angle 4.29842 / 3.05 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 497 GLU cc_start: 0.8186 (pt0) cc_final: 0.7952 (pt0) REVERT: B 235 LYS cc_start: 0.7956 (mtmp) cc_final: 0.7755 (mtmm) REVERT: B 497 GLU cc_start: 0.8162 (pt0) cc_final: 0.7935 (pt0) outliers start: 10 outliers final: 4 residues processed: 143 average time/residue: 0.5788 time to fit residues: 87.2526 Evaluate side-chains 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117247 restraints weight = 8420.830| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.62 r_work: 0.3190 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8964 Z= 0.124 Angle : 0.539 7.092 12194 Z= 0.273 Chirality : 0.042 0.122 1220 Planarity : 0.005 0.041 1552 Dihedral : 5.798 80.473 1146 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 8.86 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1048 helix: 1.17 (0.23), residues: 542 sheet: 0.91 (0.60), residues: 66 loop : -1.25 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.008 0.001 TYR B 326 PHE 0.013 0.001 PHE B 543 TRP 0.015 0.001 TRP B 430 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8964) covalent geometry : angle 0.53881 / 0.27 (12194) hydrogen bonds : bond 0.05952 / 3.97 ( 340) hydrogen bonds : angle 4.02333 / 2.84 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.218 Fit side-chains REVERT: A 118 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: A 188 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 341 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: A 497 GLU cc_start: 0.8137 (pt0) cc_final: 0.7906 (pt0) REVERT: B 118 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: B 188 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 341 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5489 (mp0) REVERT: B 497 GLU cc_start: 0.8130 (pt0) cc_final: 0.7903 (pt0) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 0.5754 time to fit residues: 81.2811 Evaluate side-chains 136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117347 restraints weight = 8537.581| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.61 r_work: 0.3191 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8964 Z= 0.130 Angle : 0.549 7.114 12194 Z= 0.278 Chirality : 0.042 0.122 1220 Planarity : 0.005 0.041 1552 Dihedral : 5.781 80.349 1146 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.94 % Allowed : 9.72 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1048 helix: 1.25 (0.23), residues: 542 sheet: 1.01 (0.60), residues: 66 loop : -1.20 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 288 TYR 0.009 0.001 TYR B 326 PHE 0.013 0.001 PHE B 543 TRP 0.016 0.001 TRP B 430 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8964) covalent geometry : angle 0.54943 / 0.28 (12194) hydrogen bonds : bond 0.05978 / 3.99 ( 340) hydrogen bonds : angle 3.95454 / 2.79 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.216 Fit side-chains REVERT: A 188 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 341 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5428 (mp0) REVERT: A 497 GLU cc_start: 0.8142 (pt0) cc_final: 0.7909 (pt0) REVERT: B 152 LYS cc_start: 0.7675 (mmtm) cc_final: 0.7318 (mmtm) REVERT: B 188 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 254 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7691 (tpp-160) REVERT: B 341 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5440 (mp0) REVERT: B 497 GLU cc_start: 0.8154 (pt0) cc_final: 0.7920 (pt0) outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.6439 time to fit residues: 87.2126 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115420 restraints weight = 8523.996| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.63 r_work: 0.3169 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8964 Z= 0.143 Angle : 0.576 7.367 12194 Z= 0.291 Chirality : 0.043 0.124 1220 Planarity : 0.005 0.042 1552 Dihedral : 5.865 81.779 1146 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.27 % Allowed : 10.37 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1048 helix: 1.21 (0.23), residues: 542 sheet: 1.07 (0.60), residues: 66 loop : -1.20 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.009 0.001 TYR B 326 PHE 0.015 0.002 PHE B 543 TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8964) covalent geometry : angle 0.57605 / 0.29 (12194) hydrogen bonds : bond 0.06445 / 4.28 ( 340) hydrogen bonds : angle 3.96340 / 2.80 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.201 Fit side-chains REVERT: A 152 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7294 (mmtm) REVERT: A 188 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 341 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5389 (mp0) REVERT: A 497 GLU cc_start: 0.8162 (pt0) cc_final: 0.7904 (pt0) REVERT: B 152 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7288 (mmtm) REVERT: B 188 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 341 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: B 497 GLU cc_start: 0.8163 (pt0) cc_final: 0.7907 (pt0) outliers start: 21 outliers final: 12 residues processed: 132 average time/residue: 0.5900 time to fit residues: 81.8188 Evaluate side-chains 136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113168 restraints weight = 8561.427| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.64 r_work: 0.3140 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8964 Z= 0.179 Angle : 0.646 8.122 12194 Z= 0.328 Chirality : 0.046 0.133 1220 Planarity : 0.006 0.043 1552 Dihedral : 6.127 87.362 1146 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.59 % Allowed : 10.37 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1048 helix: 1.05 (0.23), residues: 542 sheet: 1.09 (0.60), residues: 66 loop : -1.29 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.011 0.002 TYR A 465 PHE 0.015 0.002 PHE B 543 TRP 0.021 0.002 TRP A 430 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8964) covalent geometry : angle 0.64626 / 0.33 (12194) hydrogen bonds : bond 0.07756 / 5.15 ( 340) hydrogen bonds : angle 4.05730 / 2.87 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.340 Fit side-chains REVERT: A 110 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7390 (p0) REVERT: A 152 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7293 (mmtm) REVERT: A 188 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 341 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5375 (mp0) REVERT: A 497 GLU cc_start: 0.8172 (pt0) cc_final: 0.7871 (pt0) REVERT: B 110 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (p0) REVERT: B 152 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7318 (mmtm) REVERT: B 188 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 254 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7682 (tpp-160) REVERT: B 341 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5348 (mp0) REVERT: B 497 GLU cc_start: 0.8183 (pt0) cc_final: 0.7887 (pt0) outliers start: 24 outliers final: 7 residues processed: 131 average time/residue: 0.6453 time to fit residues: 88.9176 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 70 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115655 restraints weight = 8537.057| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.61 r_work: 0.3168 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8964 Z= 0.133 Angle : 0.570 7.841 12194 Z= 0.287 Chirality : 0.042 0.132 1220 Planarity : 0.005 0.040 1552 Dihedral : 5.968 85.223 1146 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.38 % Allowed : 10.91 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1048 helix: 1.20 (0.23), residues: 542 sheet: 1.17 (0.61), residues: 66 loop : -1.24 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 101 TYR 0.009 0.001 TYR A 326 PHE 0.014 0.001 PHE A 543 TRP 0.017 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8964) covalent geometry : angle 0.56959 / 0.29 (12194) hydrogen bonds : bond 0.06141 / 4.08 ( 340) hydrogen bonds : angle 3.96014 / 2.80 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.212 Fit side-chains REVERT: A 74 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7759 (tttm) REVERT: A 110 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (p0) REVERT: A 118 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: A 152 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7271 (mmtm) REVERT: A 188 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 222 LYS cc_start: 0.6949 (mptt) cc_final: 0.6260 (mmmt) REVERT: A 341 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5305 (mp0) REVERT: A 497 GLU cc_start: 0.8193 (pt0) cc_final: 0.7890 (pt0) REVERT: B 74 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7748 (tttm) REVERT: B 110 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7397 (p0) REVERT: B 118 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: B 152 LYS cc_start: 0.7629 (mmtm) cc_final: 0.7267 (mmtm) REVERT: B 188 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 222 LYS cc_start: 0.6972 (mptt) cc_final: 0.6279 (ptmm) REVERT: B 254 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7656 (tpp-160) REVERT: B 341 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5283 (mp0) REVERT: B 497 GLU cc_start: 0.8169 (pt0) cc_final: 0.7863 (pt0) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 0.5529 time to fit residues: 76.1978 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS A 136 GLN A 538 ASN B 36 HIS B 136 GLN B 538 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112065 restraints weight = 8570.262| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.60 r_work: 0.3107 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8964 Z= 0.219 Angle : 0.710 8.654 12194 Z= 0.362 Chirality : 0.049 0.164 1220 Planarity : 0.006 0.043 1552 Dihedral : 6.350 92.253 1146 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.16 % Allowed : 11.66 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1048 helix: 0.87 (0.22), residues: 540 sheet: 1.06 (0.60), residues: 66 loop : -1.35 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 39 TYR 0.013 0.002 TYR A 465 PHE 0.017 0.002 PHE A 543 TRP 0.021 0.002 TRP B 430 HIS 0.007 0.002 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 8964) covalent geometry : angle 0.70971 / 0.36 (12194) hydrogen bonds : bond 0.08732 / 5.80 ( 340) hydrogen bonds : angle 4.12712 / 2.92 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.330 Fit side-chains REVERT: A 110 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 152 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7324 (mmtm) REVERT: A 188 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 341 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5595 (mp0) REVERT: A 356 GLU cc_start: 0.6986 (mp0) cc_final: 0.6782 (mp0) REVERT: B 110 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7342 (p0) REVERT: B 152 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7303 (mmtm) REVERT: B 188 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 254 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7716 (tpp-160) REVERT: B 341 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5575 (mp0) REVERT: B 356 GLU cc_start: 0.6986 (mp0) cc_final: 0.6751 (mp0) REVERT: B 526 ASP cc_start: 0.7691 (t0) cc_final: 0.7488 (t0) outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.5794 time to fit residues: 84.8944 Evaluate side-chains 143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.0060 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119257 restraints weight = 8560.981| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.60 r_work: 0.3213 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8964 Z= 0.107 Angle : 0.525 8.574 12194 Z= 0.265 Chirality : 0.040 0.157 1220 Planarity : 0.005 0.038 1552 Dihedral : 5.851 83.510 1146 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.84 % Allowed : 12.42 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1048 helix: 1.30 (0.23), residues: 540 sheet: 1.31 (0.61), residues: 66 loop : -1.20 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.008 0.001 TYR A 326 PHE 0.010 0.001 PHE B 543 TRP 0.012 0.001 TRP B 299 HIS 0.002 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 8964) covalent geometry : angle 0.52485 / 0.27 (12194) hydrogen bonds : bond 0.04673 / 3.09 ( 340) hydrogen bonds : angle 3.88864 / 2.75 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.230 Fit side-chains REVERT: A 74 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7777 (tttm) REVERT: A 110 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7383 (p0) REVERT: A 222 LYS cc_start: 0.6991 (mptt) cc_final: 0.6424 (ptpp) REVERT: A 341 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5299 (mp0) REVERT: B 74 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7769 (tttm) REVERT: B 110 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 152 LYS cc_start: 0.7619 (mmtm) cc_final: 0.7283 (mmtm) REVERT: B 222 LYS cc_start: 0.6993 (mptt) cc_final: 0.6420 (ptpp) REVERT: B 254 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7711 (tpp-160) REVERT: B 341 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5248 (mp0) REVERT: B 526 ASP cc_start: 0.7585 (t0) cc_final: 0.7373 (t0) outliers start: 17 outliers final: 6 residues processed: 130 average time/residue: 0.5745 time to fit residues: 78.6853 Evaluate side-chains 135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 522 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117610 restraints weight = 8538.303| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.60 r_work: 0.3186 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8964 Z= 0.121 Angle : 0.554 9.114 12194 Z= 0.277 Chirality : 0.041 0.204 1220 Planarity : 0.005 0.037 1552 Dihedral : 5.822 82.767 1146 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.40 % Allowed : 13.28 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1048 helix: 1.37 (0.23), residues: 540 sheet: 1.31 (0.61), residues: 66 loop : -1.17 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.009 0.001 TYR B 326 PHE 0.013 0.001 PHE A 543 TRP 0.015 0.001 TRP B 430 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8964) covalent geometry : angle 0.55387 / 0.28 (12194) hydrogen bonds : bond 0.05393 / 3.58 ( 340) hydrogen bonds : angle 3.87031 / 2.75 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.290 Fit side-chains REVERT: A 74 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7801 (tttm) REVERT: A 110 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7413 (p0) REVERT: A 118 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: A 152 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7288 (mmtm) REVERT: A 222 LYS cc_start: 0.6928 (mptt) cc_final: 0.6306 (ptmm) REVERT: A 341 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5288 (mp0) REVERT: A 354 ASP cc_start: 0.6763 (t70) cc_final: 0.6500 (t0) REVERT: B 74 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7795 (tttm) REVERT: B 110 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7437 (p0) REVERT: B 118 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: B 152 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7299 (mmtm) REVERT: B 222 LYS cc_start: 0.6919 (mptt) cc_final: 0.6297 (ptmm) REVERT: B 254 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7642 (tpp-160) REVERT: B 341 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5251 (mp0) REVERT: B 356 GLU cc_start: 0.6903 (mp0) cc_final: 0.6675 (mp0) REVERT: B 526 ASP cc_start: 0.7591 (t0) cc_final: 0.7375 (t0) outliers start: 13 outliers final: 4 residues processed: 131 average time/residue: 0.5807 time to fit residues: 80.1611 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 522 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117553 restraints weight = 8492.129| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.60 r_work: 0.3191 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8964 Z= 0.122 Angle : 0.556 8.904 12194 Z= 0.278 Chirality : 0.041 0.174 1220 Planarity : 0.005 0.036 1552 Dihedral : 5.811 82.074 1146 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.19 % Allowed : 13.39 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1048 helix: 1.39 (0.23), residues: 540 sheet: 1.35 (0.61), residues: 66 loop : -1.17 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.009 0.001 TYR A 326 PHE 0.013 0.001 PHE B 543 TRP 0.015 0.001 TRP B 430 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8964) covalent geometry : angle 0.55636 / 0.28 (12194) hydrogen bonds : bond 0.05460 / 3.63 ( 340) hydrogen bonds : angle 3.85498 / 2.74 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.76 seconds wall clock time: 46 minutes 26.87 seconds (2786.87 seconds total)