Starting phenix.real_space_refine on Mon May 12 11:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4x_17429/05_2025/8p4x_17429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4x_17429/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4x_17429/05_2025/8p4x_17429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4x_17429/05_2025/8p4x_17429.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4x_17429/05_2025/8p4x_17429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4x_17429/05_2025/8p4x_17429.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.77, per 1000 atoms: 0.89 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: 1.99 Conformation dependent library (CDL) restraints added in 911.0 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: 0.77 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: 2.04 Time building geometry restraints manager: 2.35 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: 0.04 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: 1.900 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE B 543 TYR 0.012 0.001 TYR B 326 ARG 0.003 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.18388 ( 340) hydrogen bonds : angle 5.20894 ( 996) covalent geometry : bond 0.00414 ( 8964) covalent geometry : angle 0.56066 (12194) *********************** 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 : 1.027 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: 1.2983 time to fit residues: 200.1374 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.143560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122249 restraints weight = 7942.751| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.66 r_work: 0.3122 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8964 Z= 0.156 Angle : 0.615 7.584 12194 Z= 0.311 Chirality : 0.045 0.165 1220 Planarity : 0.006 0.046 1552 Dihedral : 10.268 90.212 1232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.86 % Allowed : 8.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1048 helix: 1.22 (0.24), residues: 528 sheet: 0.21 (0.58), residues: 70 loop : -1.21 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE B 543 TYR 0.009 0.002 TYR A 326 ARG 0.003 0.001 ARG A 515 Details of bonding type rmsd hydrogen bonds : bond 0.06884 ( 340) hydrogen bonds : angle 4.17694 ( 996) covalent geometry : bond 0.00341 ( 8964) covalent geometry : angle 0.61529 (12194) *********************** 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 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.928 Fit side-chains REVERT: A 200 ASP cc_start: 0.7823 (t70) cc_final: 0.7596 (t0) REVERT: A 235 LYS cc_start: 0.7909 (mtmp) cc_final: 0.7708 (mtmm) REVERT: A 497 GLU cc_start: 0.8162 (pt0) cc_final: 0.7955 (pt0) REVERT: B 200 ASP cc_start: 0.7819 (t70) cc_final: 0.7593 (t0) outliers start: 8 outliers final: 2 residues processed: 140 average time/residue: 1.4663 time to fit residues: 216.7756 Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123434 restraints weight = 8701.980| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.51 r_work: 0.3312 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8964 Z= 0.114 Angle : 0.522 6.271 12194 Z= 0.261 Chirality : 0.042 0.122 1220 Planarity : 0.005 0.039 1552 Dihedral : 9.016 99.088 1232 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.62 % Allowed : 8.53 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1048 helix: 1.34 (0.23), residues: 542 sheet: 1.09 (0.60), residues: 66 loop : -1.19 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE A 543 TYR 0.008 0.001 TYR B 298 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 340) hydrogen bonds : angle 3.93612 ( 996) covalent geometry : bond 0.00241 ( 8964) covalent geometry : angle 0.52212 (12194) *********************** 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 : 0.906 Fit side-chains REVERT: A 188 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 341 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5452 (mp0) REVERT: B 188 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 341 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5442 (mp0) outliers start: 15 outliers final: 5 residues processed: 133 average time/residue: 1.4895 time to fit residues: 208.5227 Evaluate side-chains 130 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 490 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.143556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120548 restraints weight = 8727.512| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.50 r_work: 0.3271 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8964 Z= 0.138 Angle : 0.579 7.514 12194 Z= 0.290 Chirality : 0.043 0.134 1220 Planarity : 0.005 0.040 1552 Dihedral : 9.535 108.783 1232 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 10.26 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1048 helix: 1.28 (0.23), residues: 542 sheet: 1.05 (0.60), residues: 66 loop : -1.17 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE B 543 TYR 0.009 0.001 TYR A 326 ARG 0.002 0.000 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.06364 ( 340) hydrogen bonds : angle 3.95125 ( 996) covalent geometry : bond 0.00302 ( 8964) covalent geometry : angle 0.57924 (12194) *********************** 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: 16 poor density : 125 time to evaluate : 1.032 Fit side-chains REVERT: A 118 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: A 152 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7498 (mmtm) REVERT: A 188 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 341 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5387 (mp0) REVERT: B 118 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: B 188 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 341 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5390 (mp0) outliers start: 16 outliers final: 8 residues processed: 131 average time/residue: 1.6316 time to fit residues: 224.3311 Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 307 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 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 354 ASP 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 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.145853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123145 restraints weight = 8713.749| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.50 r_work: 0.3309 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8964 Z= 0.108 Angle : 0.522 6.943 12194 Z= 0.259 Chirality : 0.041 0.119 1220 Planarity : 0.005 0.038 1552 Dihedral : 8.846 106.104 1232 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.94 % Allowed : 10.91 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1048 helix: 1.39 (0.23), residues: 542 sheet: 1.22 (0.60), residues: 66 loop : -1.06 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 430 HIS 0.003 0.001 HIS B 45 PHE 0.011 0.001 PHE B 543 TYR 0.007 0.001 TYR B 298 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 340) hydrogen bonds : angle 3.84997 ( 996) covalent geometry : bond 0.00228 ( 8964) covalent geometry : angle 0.52222 (12194) *********************** 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 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.993 Fit side-chains REVERT: A 118 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: A 152 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7451 (mmtm) REVERT: A 341 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5375 (mp0) REVERT: B 118 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: B 152 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7432 (mmtm) REVERT: B 341 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5366 (mp0) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 1.6049 time to fit residues: 221.2700 Evaluate side-chains 135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU 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 284 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 538 ASN B 36 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112899 restraints weight = 8429.790| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.60 r_work: 0.3115 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2240 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= 0.221 Angle : 0.716 9.247 12194 Z= 0.364 Chirality : 0.049 0.149 1220 Planarity : 0.006 0.044 1552 Dihedral : 11.136 116.098 1232 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 10.91 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1048 helix: 0.92 (0.22), residues: 542 sheet: 1.08 (0.60), residues: 66 loop : -1.25 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 430 HIS 0.006 0.002 HIS B 385 PHE 0.017 0.002 PHE A 543 TYR 0.013 0.002 TYR A 465 ARG 0.005 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.08842 ( 340) hydrogen bonds : angle 4.11382 ( 996) covalent geometry : bond 0.00520 ( 8964) covalent geometry : angle 0.71603 (12194) *********************** 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 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.934 Fit side-chains REVERT: A 74 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7839 (tttm) REVERT: A 110 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 118 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: A 152 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7350 (mmtm) REVERT: A 188 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8039 (mp) REVERT: A 341 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: B 110 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 118 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: B 152 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7339 (mmtm) REVERT: B 188 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8021 (mp) REVERT: B 341 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5329 (mp0) outliers start: 24 outliers final: 5 residues processed: 132 average time/residue: 1.5064 time to fit residues: 209.4193 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 : 0.909 ------------------------------------------------------------------------------- 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 341 GLU Chi-restraints excluded: chain A residue 497 GLU 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 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 497 GLU 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 85 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119640 restraints weight = 8831.362| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.51 r_work: 0.3257 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8964 Z= 0.141 Angle : 0.591 7.777 12194 Z= 0.297 Chirality : 0.044 0.145 1220 Planarity : 0.005 0.041 1552 Dihedral : 10.056 111.588 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1048 helix: 1.14 (0.23), residues: 540 sheet: 1.19 (0.60), residues: 66 loop : -1.23 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE B 543 TYR 0.009 0.001 TYR A 326 ARG 0.001 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 340) hydrogen bonds : angle 3.99405 ( 996) covalent geometry : bond 0.00311 ( 8964) covalent geometry : angle 0.59058 (12194) *********************** 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 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.923 Fit side-chains REVERT: A 74 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7924 (tttm) REVERT: A 110 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7543 (p0) REVERT: A 118 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: A 152 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7480 (mmtm) REVERT: A 222 LYS cc_start: 0.7111 (mptt) cc_final: 0.6497 (mmmt) REVERT: A 341 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5354 (mp0) REVERT: B 74 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7911 (tttm) REVERT: B 110 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7549 (p0) REVERT: B 118 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: B 152 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7479 (mmtm) REVERT: B 222 LYS cc_start: 0.7115 (mptt) cc_final: 0.6502 (mmmt) REVERT: B 341 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5373 (mp0) outliers start: 20 outliers final: 5 residues processed: 132 average time/residue: 1.6287 time to fit residues: 226.4609 Evaluate side-chains 137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 307 GLU Chi-restraints excluded: chain A residue 341 GLU 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 235 LYS Chi-restraints excluded: chain B residue 341 GLU 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 75 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.143215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120163 restraints weight = 8845.817| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.52 r_work: 0.3270 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8964 Z= 0.132 Angle : 0.572 8.194 12194 Z= 0.286 Chirality : 0.043 0.146 1220 Planarity : 0.005 0.039 1552 Dihedral : 9.632 110.760 1232 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.84 % Allowed : 12.31 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1048 helix: 1.25 (0.23), residues: 540 sheet: 1.23 (0.61), residues: 66 loop : -1.19 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.013 0.001 PHE A 543 TYR 0.010 0.001 TYR B 326 ARG 0.001 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.06024 ( 340) hydrogen bonds : angle 3.94777 ( 996) covalent geometry : bond 0.00288 ( 8964) covalent geometry : angle 0.57235 (12194) *********************** 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 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.923 Fit side-chains REVERT: A 110 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7508 (p0) REVERT: A 118 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: A 152 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7504 (mmtm) REVERT: A 188 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 222 LYS cc_start: 0.7061 (mptt) cc_final: 0.6487 (mmmt) REVERT: A 341 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: A 354 ASP cc_start: 0.6574 (t70) cc_final: 0.6248 (t0) REVERT: A 526 ASP cc_start: 0.7777 (t0) cc_final: 0.7560 (t0) REVERT: B 110 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7527 (p0) REVERT: B 118 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: B 152 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7498 (mmtm) REVERT: B 188 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 222 LYS cc_start: 0.7053 (mptt) cc_final: 0.6480 (mmmt) REVERT: B 341 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5339 (mp0) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 1.5571 time to fit residues: 213.1695 Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 307 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU 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 235 LYS Chi-restraints excluded: chain B residue 307 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 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119297 restraints weight = 8851.837| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.51 r_work: 0.3257 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8964 Z= 0.147 Angle : 0.606 8.422 12194 Z= 0.305 Chirality : 0.044 0.176 1220 Planarity : 0.005 0.040 1552 Dihedral : 9.888 112.969 1232 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.27 % Allowed : 11.77 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1048 helix: 1.19 (0.23), residues: 540 sheet: 1.22 (0.61), residues: 66 loop : -1.22 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS B 45 PHE 0.013 0.002 PHE B 543 TYR 0.010 0.001 TYR A 326 ARG 0.002 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.06594 ( 340) hydrogen bonds : angle 3.99821 ( 996) covalent geometry : bond 0.00327 ( 8964) covalent geometry : angle 0.60648 (12194) *********************** 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 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.006 Fit side-chains REVERT: A 74 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7916 (tttm) REVERT: A 110 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 118 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: A 152 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7498 (mmtm) REVERT: A 188 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 222 LYS cc_start: 0.7072 (mptt) cc_final: 0.6507 (mmmt) REVERT: A 341 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: A 354 ASP cc_start: 0.6761 (t70) cc_final: 0.6450 (t0) REVERT: B 74 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7908 (tttm) REVERT: B 110 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7551 (p0) REVERT: B 118 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: B 152 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7466 (mmtm) REVERT: B 188 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 254 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7796 (tpp-160) REVERT: B 341 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5363 (mp0) outliers start: 21 outliers final: 9 residues processed: 128 average time/residue: 1.5590 time to fit residues: 209.8463 Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 307 GLU 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 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 538 ASN B 36 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124653 restraints weight = 8797.784| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.51 r_work: 0.3329 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8964 Z= 0.100 Angle : 0.515 8.995 12194 Z= 0.256 Chirality : 0.040 0.157 1220 Planarity : 0.005 0.036 1552 Dihedral : 8.343 104.290 1232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.51 % Allowed : 12.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1048 helix: 1.41 (0.23), residues: 542 sheet: 1.32 (0.61), residues: 66 loop : -1.04 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 299 HIS 0.002 0.001 HIS B 45 PHE 0.009 0.001 PHE B 543 TYR 0.007 0.001 TYR A 326 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 340) hydrogen bonds : angle 3.83464 ( 996) covalent geometry : bond 0.00214 ( 8964) covalent geometry : angle 0.51525 (12194) ********************** 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 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.003 Fit side-chains REVERT: A 152 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7396 (mmtm) REVERT: A 188 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 222 LYS cc_start: 0.7045 (mptt) cc_final: 0.6507 (ptmm) REVERT: A 254 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7727 (tpp-160) REVERT: A 341 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5319 (mp0) REVERT: A 354 ASP cc_start: 0.6523 (t70) cc_final: 0.6182 (t0) REVERT: A 356 GLU cc_start: 0.7021 (mp0) cc_final: 0.6738 (mp0) REVERT: B 152 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7421 (mmtm) REVERT: B 188 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7962 (mp) REVERT: B 222 LYS cc_start: 0.7008 (mptt) cc_final: 0.6457 (ptmm) REVERT: B 254 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7717 (tpp-160) REVERT: B 341 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5380 (mp0) outliers start: 14 outliers final: 2 residues processed: 128 average time/residue: 1.6166 time to fit residues: 217.5799 Evaluate side-chains 130 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 188 LEU 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 4 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118031 restraints weight = 8763.345| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.50 r_work: 0.3242 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8964 Z= 0.177 Angle : 0.657 8.732 12194 Z= 0.330 Chirality : 0.046 0.172 1220 Planarity : 0.005 0.039 1552 Dihedral : 10.261 115.171 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.97 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1048 helix: 1.18 (0.23), residues: 540 sheet: 1.23 (0.61), residues: 66 loop : -1.20 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 430 HIS 0.005 0.001 HIS A 45 PHE 0.014 0.002 PHE B 543 TYR 0.011 0.002 TYR B 465 ARG 0.004 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.07483 ( 340) hydrogen bonds : angle 4.00103 ( 996) covalent geometry : bond 0.00406 ( 8964) covalent geometry : angle 0.65712 (12194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6778.95 seconds wall clock time: 117 minutes 6.70 seconds (7026.70 seconds total)