Starting phenix.real_space_refine on Sat Aug 23 01:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_17429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_17429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_17429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_17429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4x_17429/08_2025/8p4x_17429.map" } 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): 0.01s 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: 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: 2.74, per 1000 atoms: 0.31 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: 0.79 Conformation dependent library (CDL) restraints added in 299.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.23 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: 0.88 Time building geometry restraints manager: 1.04 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: 5002 18.12 - 36.25: 212 36.25 - 54.37: 62 54.37 - 72.50: 30 72.50 - 90.62: 12 Dihedral angle restraints: 5318 sinusoidal: 2270 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 5315 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: 2.650 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.050 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 13.116 90.621 3362 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 aren 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 covalent geometry : bond 0.00414 ( 8964) covalent geometry : angle 0.56066 (12194) hydrogen bonds : bond 0.18388 ( 340) hydrogen bonds : angle 5.20894 ( 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 : 0.339 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: 0.6335 time to fit residues: 97.3829 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 : 0.370 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3556 r_free = 0.3556 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115715 restraints weight = 7992.805| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.16 r_work: 0.3031 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8964 Z= 0.209 Angle : 0.697 8.093 12194 Z= 0.358 Chirality : 0.049 0.149 1220 Planarity : 0.006 0.051 1552 Dihedral : 11.039 95.289 1232 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 8.21 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.25), residues: 1048 helix: 0.84 (0.23), residues: 542 sheet: 0.51 (0.59), residues: 66 loop : -1.34 (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 0.002 PHE B 543 TRP 0.020 0.002 TRP B 430 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8964) covalent geometry : angle 0.69687 (12194) hydrogen bonds : bond 0.08778 ( 340) hydrogen bonds : angle 4.30489 ( 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 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.7789 (t70) cc_final: 0.7583 (t0) REVERT: A 497 GLU cc_start: 0.8131 (pt0) cc_final: 0.7897 (pt0) REVERT: B 200 ASP cc_start: 0.7790 (t70) cc_final: 0.7584 (t0) REVERT: B 497 GLU cc_start: 0.8143 (pt0) cc_final: 0.7915 (pt0) outliers start: 10 outliers final: 6 residues processed: 145 average time/residue: 0.7599 time to fit residues: 116.0014 Evaluate side-chains 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 429 MET 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: 0.0980 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.142632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117446 restraints weight = 8403.951| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.61 r_work: 0.3199 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1798 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= 0.126 Angle : 0.551 7.012 12194 Z= 0.276 Chirality : 0.042 0.124 1220 Planarity : 0.005 0.042 1552 Dihedral : 9.691 100.301 1232 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.62 % Allowed : 8.75 % Favored : 89.63 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1048 helix: 1.16 (0.23), residues: 542 sheet: 0.85 (0.59), residues: 66 loop : -1.25 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.008 0.001 TYR B 326 PHE 0.013 0.001 PHE A 543 TRP 0.015 0.001 TRP B 430 HIS 0.004 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8964) covalent geometry : angle 0.55068 (12194) hydrogen bonds : bond 0.05993 ( 340) hydrogen bonds : angle 4.02370 ( 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 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.357 Fit side-chains REVERT: A 118 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: A 188 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 200 ASP cc_start: 0.7668 (t70) cc_final: 0.7423 (t0) REVERT: A 341 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5498 (mp0) REVERT: A 497 GLU cc_start: 0.8128 (pt0) cc_final: 0.7899 (pt0) REVERT: B 118 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: B 188 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 200 ASP cc_start: 0.7663 (t70) cc_final: 0.7424 (t0) REVERT: B 341 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5497 (mp0) REVERT: B 497 GLU cc_start: 0.8118 (pt0) cc_final: 0.7895 (pt0) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 0.7853 time to fit residues: 108.9120 Evaluate side-chains 134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 522 SER 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: 0.0980 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.139580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114064 restraints weight = 8549.384| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.64 r_work: 0.3148 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8964 Z= 0.169 Angle : 0.635 8.167 12194 Z= 0.320 Chirality : 0.046 0.150 1220 Planarity : 0.006 0.043 1552 Dihedral : 10.483 111.724 1232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 aren not related in a simple way. whole: 0.14 (0.25), residues: 1048 helix: 1.05 (0.23), residues: 542 sheet: 0.95 (0.59), residues: 66 loop : -1.25 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.010 0.002 TYR B 465 PHE 0.015 0.002 PHE B 543 TRP 0.020 0.002 TRP B 430 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8964) covalent geometry : angle 0.63462 (12194) hydrogen bonds : bond 0.07510 ( 340) hydrogen bonds : angle 4.06158 ( 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 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.367 Fit side-chains REVERT: A 118 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: A 152 LYS cc_start: 0.7695 (mmtm) cc_final: 0.7316 (mmtm) REVERT: A 188 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 200 ASP cc_start: 0.7691 (t70) cc_final: 0.7490 (t0) REVERT: A 341 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5433 (mp0) REVERT: A 497 GLU cc_start: 0.8136 (pt0) cc_final: 0.7877 (pt0) REVERT: B 118 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: B 188 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 254 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7667 (tpp-160) REVERT: B 256 MET cc_start: 0.8171 (mtp) cc_final: 0.7884 (mtp) REVERT: B 341 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: B 497 GLU cc_start: 0.8136 (pt0) cc_final: 0.7875 (pt0) outliers start: 18 outliers final: 7 residues processed: 129 average time/residue: 0.7941 time to fit residues: 107.6272 Evaluate side-chains 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 A residue 490 LYS 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 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 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: 1.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3548 r_free = 0.3548 target = 0.139377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113973 restraints weight = 8568.329| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.64 r_work: 0.3144 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8964 Z= 0.165 Angle : 0.628 7.918 12194 Z= 0.316 Chirality : 0.045 0.137 1220 Planarity : 0.006 0.043 1552 Dihedral : 10.407 113.290 1232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.02 % Allowed : 10.69 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1048 helix: 1.05 (0.23), residues: 542 sheet: 1.08 (0.60), residues: 66 loop : -1.28 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.010 0.002 TYR A 326 PHE 0.015 0.002 PHE B 543 TRP 0.020 0.002 TRP B 430 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8964) covalent geometry : angle 0.62769 (12194) hydrogen bonds : bond 0.07248 ( 340) hydrogen bonds : angle 4.02867 ( 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 155 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.361 Fit side-chains REVERT: A 110 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7368 (p0) REVERT: A 118 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: A 152 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7283 (mmtm) REVERT: A 188 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 200 ASP cc_start: 0.7690 (t70) cc_final: 0.7488 (t0) REVERT: A 341 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5345 (mp0) REVERT: A 497 GLU cc_start: 0.8172 (pt0) cc_final: 0.7876 (pt0) REVERT: B 110 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7392 (p0) REVERT: B 118 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: B 152 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7314 (mmtm) REVERT: B 188 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 254 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7645 (tpp-160) REVERT: B 341 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5333 (mp0) REVERT: B 497 GLU cc_start: 0.8141 (pt0) cc_final: 0.7855 (pt0) outliers start: 28 outliers final: 14 residues processed: 138 average time/residue: 0.7015 time to fit residues: 101.8902 Evaluate side-chains 148 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 490 LYS 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 235 LYS Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU 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: 7.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3543 r_free = 0.3543 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113479 restraints weight = 8588.948| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.62 r_work: 0.3137 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2229 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= 0.186 Angle : 0.661 8.609 12194 Z= 0.333 Chirality : 0.046 0.149 1220 Planarity : 0.006 0.043 1552 Dihedral : 10.737 115.705 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.81 % Allowed : 10.37 % Favored : 86.83 % 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 aren not related in a simple way. whole: 0.04 (0.25), residues: 1048 helix: 0.95 (0.22), residues: 542 sheet: 1.06 (0.60), residues: 66 loop : -1.32 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.011 0.002 TYR A 465 PHE 0.016 0.002 PHE B 543 TRP 0.020 0.002 TRP A 430 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8964) covalent geometry : angle 0.66118 (12194) hydrogen bonds : bond 0.07898 ( 340) hydrogen bonds : angle 4.07089 ( 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 152 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.352 Fit side-chains REVERT: A 74 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7826 (tttm) REVERT: A 110 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7378 (p0) REVERT: A 118 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: A 152 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7307 (mmtm) REVERT: A 188 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 341 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5362 (mp0) REVERT: B 74 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7827 (tttm) REVERT: B 110 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7392 (p0) REVERT: B 118 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: B 152 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7317 (mmtm) REVERT: B 188 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 254 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7684 (tpp-160) REVERT: B 341 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: B 497 GLU cc_start: 0.8160 (pt0) cc_final: 0.7840 (pt0) outliers start: 26 outliers final: 16 residues processed: 138 average time/residue: 0.7472 time to fit residues: 108.3762 Evaluate side-chains 152 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 486 GLU Chi-restraints excluded: chain A residue 490 LYS 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 235 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3633 r_free = 0.3633 target = 0.145455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122842 restraints weight = 8794.598| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.51 r_work: 0.3313 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8964 Z= 0.108 Angle : 0.523 7.959 12194 Z= 0.260 Chirality : 0.041 0.121 1220 Planarity : 0.005 0.038 1552 Dihedral : 9.011 106.517 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.27 % Allowed : 11.56 % 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 aren not related in a simple way. whole: 0.48 (0.26), residues: 1048 helix: 1.35 (0.23), residues: 542 sheet: 1.29 (0.61), residues: 66 loop : -1.18 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.007 0.001 TYR B 326 PHE 0.012 0.001 PHE B 543 TRP 0.012 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8964) covalent geometry : angle 0.52349 (12194) hydrogen bonds : bond 0.04785 ( 340) hydrogen bonds : angle 3.85023 ( 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 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.295 Fit side-chains REVERT: A 74 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7963 (tttm) REVERT: A 110 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7513 (p0) REVERT: A 152 LYS cc_start: 0.7722 (mmtm) cc_final: 0.7454 (mmtm) REVERT: A 188 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 222 LYS cc_start: 0.7164 (mptt) cc_final: 0.6642 (ptmm) REVERT: A 254 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7752 (tpp-160) REVERT: A 341 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5412 (mp0) REVERT: B 74 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7963 (tttm) REVERT: B 110 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7518 (p0) REVERT: B 152 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7464 (mmtm) REVERT: B 188 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7974 (mp) REVERT: B 222 LYS cc_start: 0.7154 (mptt) cc_final: 0.6582 (mmmt) REVERT: B 254 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7714 (tpp-160) REVERT: B 341 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5382 (mp0) outliers start: 21 outliers final: 4 residues processed: 129 average time/residue: 0.7581 time to fit residues: 102.3696 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 235 LYS Chi-restraints excluded: chain A residue 254 ARG 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 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 538 ASN B 136 GLN B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113942 restraints weight = 8551.398| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.60 r_work: 0.3142 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8964 Z= 0.181 Angle : 0.650 8.579 12194 Z= 0.327 Chirality : 0.046 0.152 1220 Planarity : 0.006 0.040 1552 Dihedral : 10.406 115.209 1232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.48 % Allowed : 11.77 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1048 helix: 1.15 (0.23), residues: 540 sheet: 1.19 (0.61), residues: 66 loop : -1.28 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.011 0.002 TYR A 465 PHE 0.015 0.002 PHE A 543 TRP 0.019 0.002 TRP B 430 HIS 0.005 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8964) covalent geometry : angle 0.65037 (12194) hydrogen bonds : bond 0.07598 ( 340) hydrogen bonds : angle 4.00343 ( 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 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.217 Fit side-chains REVERT: A 74 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7863 (tttm) REVERT: A 110 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7407 (p0) REVERT: A 152 LYS cc_start: 0.7657 (mmtm) cc_final: 0.7308 (mmtm) REVERT: A 188 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 254 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7696 (tpp-160) REVERT: A 341 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: B 74 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7857 (tttm) REVERT: B 110 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7427 (p0) REVERT: B 152 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7317 (mmtm) REVERT: B 188 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 254 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7680 (tpp-160) REVERT: B 341 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5293 (mp0) outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 0.7426 time to fit residues: 101.3469 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 254 ARG Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 522 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 235 LYS Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU 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: 0.1980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.0170 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3623 r_free = 0.3623 target = 0.144565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121727 restraints weight = 8781.000| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.51 r_work: 0.3295 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8964 Z= 0.114 Angle : 0.539 8.518 12194 Z= 0.268 Chirality : 0.041 0.122 1220 Planarity : 0.005 0.037 1552 Dihedral : 9.244 108.850 1232 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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 aren not related in a simple way. whole: 0.46 (0.26), residues: 1048 helix: 1.33 (0.23), residues: 542 sheet: 1.30 (0.62), residues: 66 loop : -1.18 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.008 0.001 TYR A 326 PHE 0.012 0.001 PHE A 543 TRP 0.013 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8964) covalent geometry : angle 0.53857 (12194) hydrogen bonds : bond 0.05200 ( 340) hydrogen bonds : angle 3.85600 ( 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 : 0.355 Fit side-chains REVERT: A 110 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7526 (p0) REVERT: A 118 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: A 152 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7433 (mmtm) REVERT: A 188 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 222 LYS cc_start: 0.7136 (mptt) cc_final: 0.6602 (ptpp) REVERT: A 254 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7711 (tpp-160) REVERT: A 341 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5338 (mp0) REVERT: B 110 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 118 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: B 152 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7438 (mmtm) REVERT: B 188 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8000 (mp) REVERT: B 222 LYS cc_start: 0.7125 (mptt) cc_final: 0.6534 (ptmm) REVERT: B 254 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7703 (tpp-160) REVERT: B 341 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5313 (mp0) outliers start: 17 outliers final: 5 residues processed: 127 average time/residue: 0.8159 time to fit residues: 108.7403 Evaluate side-chains 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 235 LYS Chi-restraints excluded: chain A residue 254 ARG 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 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS 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 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 538 ASN B 136 GLN B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122880 restraints weight = 8701.954| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.50 r_work: 0.3304 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8964 Z= 0.112 Angle : 0.539 8.844 12194 Z= 0.265 Chirality : 0.041 0.120 1220 Planarity : 0.005 0.037 1552 Dihedral : 8.590 107.199 1232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 13.07 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1048 helix: 1.41 (0.23), residues: 542 sheet: 1.29 (0.62), residues: 66 loop : -1.11 (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 A 326 PHE 0.012 0.001 PHE A 543 TRP 0.014 0.001 TRP B 430 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8964) covalent geometry : angle 0.53864 (12194) hydrogen bonds : bond 0.04925 ( 340) hydrogen bonds : angle 3.80590 ( 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 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.353 Fit side-chains REVERT: A 74 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8001 (tttm) REVERT: A 110 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7507 (p0) REVERT: A 152 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7449 (mmtm) REVERT: A 188 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 222 LYS cc_start: 0.7079 (mptt) cc_final: 0.6559 (ptpp) REVERT: A 254 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7742 (tpp-160) REVERT: A 341 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5365 (mp0) REVERT: B 74 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7999 (tttm) REVERT: B 110 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7525 (p0) REVERT: B 152 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7459 (mmtm) REVERT: B 188 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 222 LYS cc_start: 0.7064 (mptt) cc_final: 0.6538 (ptpp) REVERT: B 254 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7718 (tpp-160) REVERT: B 341 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5360 (mp0) outliers start: 15 outliers final: 5 residues processed: 130 average time/residue: 0.8283 time to fit residues: 112.8317 Evaluate side-chains 137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 235 LYS Chi-restraints excluded: chain A residue 254 ARG 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 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 341 GLU 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: 0.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3622 r_free = 0.3622 target = 0.144324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121510 restraints weight = 8686.993| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.50 r_work: 0.3292 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2317 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 : 0.559 9.001 12194 Z= 0.276 Chirality : 0.042 0.134 1220 Planarity : 0.005 0.037 1552 Dihedral : 8.828 109.465 1232 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.62 % Allowed : 12.96 % 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 aren not related in a simple way. whole: 0.54 (0.26), residues: 1048 helix: 1.37 (0.23), residues: 542 sheet: 1.31 (0.62), residues: 66 loop : -1.10 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 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 A 45 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8964) covalent geometry : angle 0.55870 (12194) hydrogen bonds : bond 0.05373 ( 340) hydrogen bonds : angle 3.83015 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.91 seconds wall clock time: 55 minutes 24.73 seconds (3324.73 seconds total)