Starting phenix.real_space_refine on Thu Jul 2 17:25:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz1_13118/07_2026/7oz1_13118.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 5864 2.51 5 N 1414 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "B" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 1.51, per 1000 atoms: 0.17 Number of scatterers: 8942 At special positions: 0 Unit cell: (78.54, 104.94, 123.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 1588 8.00 N 1414 7.00 C 5864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.04 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.04 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: 0.88 Conformation dependent library (CDL) restraints added in 293.8 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 60.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.633A pdb=" N ALA A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.697A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 586' Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 636 through 664 removed outlier: 3.740A pdb=" N PHE A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.632A pdb=" N ALA B 210 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 211' Processing helix chain 'B' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix Processing helix chain 'B' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.696A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 586' Processing helix chain 'B' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 636 through 664 removed outlier: 3.741A pdb=" N PHE B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE A 104 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU A 82 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS A 140 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161 removed outlier: 6.752A pdb=" N CYS A 160 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN A 286 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 7.006A pdb=" N VAL A 289 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE B 104 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU B 82 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 140 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.751A pdb=" N CYS B 160 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 286 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291 removed outlier: 7.007A pdb=" N VAL B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1397 1.32 - 1.45: 2380 1.45 - 1.57: 5245 1.57 - 1.70: 14 1.70 - 1.83: 110 Bond restraints: 9146 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C8 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.20e+01 ... (remaining 9141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 12322 3.66 - 7.33: 72 7.33 - 10.99: 8 10.99 - 14.65: 0 14.65 - 18.31: 6 Bond angle restraints: 12408 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" N PRO A 276 " pdb=" CA PRO A 276 " pdb=" C PRO A 276 " ideal model delta sigma weight residual 112.47 94.16 18.31 2.06e+00 2.36e-01 7.90e+01 ... (remaining 12403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 4552 16.09 - 32.17: 607 32.17 - 48.26: 139 48.26 - 64.35: 32 64.35 - 80.44: 12 Dihedral angle restraints: 5342 sinusoidal: 2200 harmonic: 3142 Sorted by residual: dihedral pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " pdb=" SG CYS A 617 " pdb=" CB CYS A 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.47 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS B 617 " pdb=" CB CYS B 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.49 -40.51 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CA LEU A 609 " pdb=" C LEU A 609 " pdb=" N HIS A 610 " pdb=" CA HIS A 610 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1238 0.070 - 0.140: 167 0.140 - 0.210: 19 0.210 - 0.280: 4 0.280 - 0.350: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" C PRO A 276 " pdb=" CB PRO A 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PRO B 276 " pdb=" N PRO B 276 " pdb=" C PRO B 276 " pdb=" CB PRO B 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CBE Y01 B 702 " pdb=" CAP Y01 B 702 " pdb=" CBB Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1427 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 277 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C SER B 277 " -0.061 2.00e-02 2.50e+03 pdb=" O SER B 277 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA B 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 277 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C SER A 277 " 0.060 2.00e-02 2.50e+03 pdb=" O SER A 277 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A 278 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 459 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 460 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.029 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 119 2.67 - 3.23: 8739 3.23 - 3.78: 13178 3.78 - 4.34: 17986 4.34 - 4.90: 28954 Nonbonded interactions: 68976 Sorted by model distance: nonbonded pdb=" OG SER B 125 " pdb=" O1B ATP B 701 " model vdw 2.109 3.040 nonbonded pdb=" OG SER A 125 " pdb=" O1B ATP A 701 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR B 297 " pdb=" O LYS B 300 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR A 297 " pdb=" O LYS A 300 " model vdw 2.160 3.040 nonbonded pdb=" O LEU B 550 " pdb=" OG1 THR B 554 " model vdw 2.251 3.040 ... (remaining 68971 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' and resid 74 through 704) selection = (chain 'B' and resid 74 through 704) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.006 0.083 9148 Z= 0.371 Angle : 0.917 18.314 12412 Z= 0.584 Chirality : 0.051 0.350 1430 Planarity : 0.004 0.051 1490 Dihedral : 15.429 80.437 3324 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.21 % Allowed : 7.51 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.23), residues: 1076 helix: -1.39 (0.18), residues: 602 sheet: -1.84 (0.63), residues: 74 loop : -3.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.009 0.001 TYR B 481 PHE 0.012 0.002 PHE B 646 TRP 0.012 0.002 TRP B 480 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.37 ( 9146) covalent geometry : angle 0.91630 / 0.58 (12408) SS BOND : bond 0.00889 / 0.45 ( 2) SS BOND : angle 2.10572 / 1.26 ( 4) hydrogen bonds : bond 0.11285 / 7.96 ( 454) hydrogen bonds : angle 5.31263 / 3.69 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8493 (tpp) cc_final: 0.8029 (tpt) REVERT: A 259 MET cc_start: 0.8671 (ttm) cc_final: 0.8359 (ttm) REVERT: A 492 MET cc_start: 0.7730 (mmm) cc_final: 0.7334 (mtp) REVERT: A 511 TRP cc_start: 0.8125 (m100) cc_final: 0.7833 (m-10) REVERT: A 609 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp) REVERT: B 179 MET cc_start: 0.8477 (tpp) cc_final: 0.7954 (tpt) REVERT: B 259 MET cc_start: 0.8654 (ttm) cc_final: 0.8327 (ttm) REVERT: B 492 MET cc_start: 0.7721 (mmm) cc_final: 0.7368 (mtp) REVERT: B 511 TRP cc_start: 0.8110 (m100) cc_final: 0.7852 (m-10) REVERT: B 609 LEU cc_start: 0.8582 (tp) cc_final: 0.8366 (tp) outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.0787 time to fit residues: 21.3812 Evaluate side-chains 142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0070 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 418 HIS B 175 GLN B 336 GLN B 418 HIS B 633 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122026 restraints weight = 12486.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124494 restraints weight = 8236.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126383 restraints weight = 5980.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127507 restraints weight = 4669.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128549 restraints weight = 3904.383| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9148 Z= 0.121 Angle : 0.621 5.810 12412 Z= 0.305 Chirality : 0.040 0.147 1430 Planarity : 0.004 0.031 1490 Dihedral : 10.771 88.926 1350 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.18 % Allowed : 15.77 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.25), residues: 1076 helix: 0.04 (0.21), residues: 612 sheet: -1.62 (0.58), residues: 74 loop : -2.84 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 298 TYR 0.008 0.001 TYR B 134 PHE 0.017 0.002 PHE B 281 TRP 0.011 0.001 TRP A 480 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9146) covalent geometry : angle 0.62030 / 0.30 (12408) SS BOND : bond 0.00899 / 0.45 ( 2) SS BOND : angle 1.75688 / 1.06 ( 4) hydrogen bonds : bond 0.03757 / 2.49 ( 454) hydrogen bonds : angle 4.30101 / 2.98 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7975 (mmm) cc_final: 0.7439 (mmm) REVERT: A 179 MET cc_start: 0.8638 (tpp) cc_final: 0.8324 (tpt) REVERT: A 277 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 298 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7770 (tmm-80) REVERT: A 404 ILE cc_start: 0.7991 (tt) cc_final: 0.7615 (mt) REVERT: A 407 ASP cc_start: 0.8204 (t0) cc_final: 0.7965 (t0) REVERT: A 446 LEU cc_start: 0.8229 (tp) cc_final: 0.7916 (tp) REVERT: A 492 MET cc_start: 0.7738 (mmm) cc_final: 0.7251 (mtp) REVERT: A 511 TRP cc_start: 0.7904 (m100) cc_final: 0.7603 (m-10) REVERT: A 609 LEU cc_start: 0.8472 (tp) cc_final: 0.8216 (tp) REVERT: B 178 MET cc_start: 0.7943 (mmm) cc_final: 0.7339 (mmm) REVERT: B 179 MET cc_start: 0.8620 (tpp) cc_final: 0.8186 (tpt) REVERT: B 298 ARG cc_start: 0.8340 (tmm-80) cc_final: 0.8130 (ttt180) REVERT: B 404 ILE cc_start: 0.8005 (tt) cc_final: 0.7651 (mt) REVERT: B 407 ASP cc_start: 0.8161 (t0) cc_final: 0.7921 (t0) REVERT: B 446 LEU cc_start: 0.8204 (tp) cc_final: 0.7879 (tp) REVERT: B 454 MET cc_start: 0.8138 (ttp) cc_final: 0.7917 (tmm) REVERT: B 492 MET cc_start: 0.7739 (mmm) cc_final: 0.7218 (mtp) REVERT: B 511 TRP cc_start: 0.7869 (m100) cc_final: 0.7598 (m-10) outliers start: 11 outliers final: 6 residues processed: 164 average time/residue: 0.0772 time to fit residues: 18.0219 Evaluate side-chains 145 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN A 418 HIS B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118938 restraints weight = 12649.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121605 restraints weight = 8167.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123497 restraints weight = 5852.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124811 restraints weight = 4536.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125726 restraints weight = 3709.259| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9148 Z= 0.135 Angle : 0.591 5.666 12412 Z= 0.290 Chirality : 0.040 0.141 1430 Planarity : 0.004 0.030 1490 Dihedral : 10.252 82.360 1350 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.72 % Allowed : 18.35 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1076 helix: 0.50 (0.21), residues: 616 sheet: -1.61 (0.57), residues: 74 loop : -2.61 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 345 TYR 0.007 0.001 TYR B 288 PHE 0.017 0.001 PHE B 281 TRP 0.006 0.001 TRP A 583 HIS 0.006 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9146) covalent geometry : angle 0.59020 / 0.29 (12408) SS BOND : bond 0.00686 / 0.35 ( 2) SS BOND : angle 1.37507 / 0.86 ( 4) hydrogen bonds : bond 0.03579 / 2.37 ( 454) hydrogen bonds : angle 4.12702 / 2.85 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.214 Fit side-chains REVERT: A 179 MET cc_start: 0.8640 (tpp) cc_final: 0.8350 (tpt) REVERT: A 404 ILE cc_start: 0.8020 (tt) cc_final: 0.7698 (mt) REVERT: A 492 MET cc_start: 0.7671 (mmm) cc_final: 0.7214 (mtp) REVERT: A 511 TRP cc_start: 0.7992 (m100) cc_final: 0.7614 (m-10) REVERT: B 179 MET cc_start: 0.8610 (tpp) cc_final: 0.8203 (tpt) REVERT: B 298 ARG cc_start: 0.8374 (tmm-80) cc_final: 0.8155 (ttt180) REVERT: B 404 ILE cc_start: 0.8040 (tt) cc_final: 0.7720 (mt) REVERT: B 492 MET cc_start: 0.7726 (mmm) cc_final: 0.7265 (mtp) REVERT: B 511 TRP cc_start: 0.7936 (m100) cc_final: 0.7616 (m-10) REVERT: B 609 LEU cc_start: 0.8263 (tp) cc_final: 0.8024 (tp) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.0662 time to fit residues: 14.9447 Evaluate side-chains 149 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 657 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 19 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 418 HIS A 618 HIS B 264 GLN B 418 HIS B 582 GLN B 618 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121873 restraints weight = 12746.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124377 restraints weight = 8219.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126213 restraints weight = 5892.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127368 restraints weight = 4596.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128356 restraints weight = 3810.688| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9148 Z= 0.106 Angle : 0.572 6.068 12412 Z= 0.278 Chirality : 0.039 0.135 1430 Planarity : 0.003 0.032 1490 Dihedral : 9.900 78.451 1350 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.25 % Allowed : 19.53 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1076 helix: 0.82 (0.22), residues: 622 sheet: -1.38 (0.56), residues: 74 loop : -2.45 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.024 0.001 TYR A 297 PHE 0.010 0.001 PHE B 284 TRP 0.007 0.001 TRP A 583 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9146) covalent geometry : angle 0.57163 / 0.28 (12408) SS BOND : bond 0.00710 / 0.36 ( 2) SS BOND : angle 1.28766 / 0.78 ( 4) hydrogen bonds : bond 0.03256 / 2.15 ( 454) hydrogen bonds : angle 3.99374 / 2.74 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.320 Fit side-chains REVERT: A 178 MET cc_start: 0.7969 (mmm) cc_final: 0.7438 (mmm) REVERT: A 404 ILE cc_start: 0.7950 (tt) cc_final: 0.7700 (mt) REVERT: A 405 MET cc_start: 0.8279 (tmm) cc_final: 0.7867 (tmm) REVERT: A 492 MET cc_start: 0.7600 (mmm) cc_final: 0.7153 (mtp) REVERT: A 511 TRP cc_start: 0.7872 (m100) cc_final: 0.7429 (m-10) REVERT: A 660 TYR cc_start: 0.8012 (t80) cc_final: 0.7627 (t80) REVERT: B 178 MET cc_start: 0.7897 (mmm) cc_final: 0.7326 (mmm) REVERT: B 179 MET cc_start: 0.8590 (tpp) cc_final: 0.8330 (tpt) REVERT: B 277 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7941 (p) REVERT: B 404 ILE cc_start: 0.7957 (tt) cc_final: 0.7705 (mt) REVERT: B 405 MET cc_start: 0.8332 (tmm) cc_final: 0.7906 (tmm) REVERT: B 492 MET cc_start: 0.7712 (mmm) cc_final: 0.7272 (mtp) REVERT: B 511 TRP cc_start: 0.7840 (m100) cc_final: 0.7400 (m-10) REVERT: B 660 TYR cc_start: 0.7972 (t80) cc_final: 0.7559 (t80) outliers start: 21 outliers final: 13 residues processed: 163 average time/residue: 0.0646 time to fit residues: 15.8454 Evaluate side-chains 144 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 171 HIS A 418 HIS B 164 GLN B 171 HIS B 418 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116221 restraints weight = 12864.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118543 restraints weight = 8477.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120193 restraints weight = 6187.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121162 restraints weight = 4879.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122045 restraints weight = 4139.792| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9148 Z= 0.227 Angle : 0.678 6.463 12412 Z= 0.332 Chirality : 0.043 0.146 1430 Planarity : 0.004 0.033 1490 Dihedral : 9.956 74.533 1350 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.43 % Allowed : 18.99 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.26), residues: 1076 helix: 0.59 (0.21), residues: 632 sheet: -1.60 (0.56), residues: 74 loop : -2.70 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.027 0.002 TYR B 297 PHE 0.012 0.002 PHE A 281 TRP 0.003 0.001 TRP A 480 HIS 0.010 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 ( 9146) covalent geometry : angle 0.67743 / 0.33 (12408) SS BOND : bond 0.00459 / 0.23 ( 2) SS BOND : angle 1.31309 / 0.80 ( 4) hydrogen bonds : bond 0.03907 / 2.54 ( 454) hydrogen bonds : angle 4.21153 / 2.91 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.298 Fit side-chains REVERT: A 178 MET cc_start: 0.7996 (mmm) cc_final: 0.7351 (mmm) REVERT: A 404 ILE cc_start: 0.8022 (tt) cc_final: 0.7748 (mt) REVERT: A 492 MET cc_start: 0.7730 (mmm) cc_final: 0.7338 (mtp) REVERT: A 511 TRP cc_start: 0.8058 (m100) cc_final: 0.7608 (m-10) REVERT: B 178 MET cc_start: 0.8028 (mmm) cc_final: 0.7372 (mmm) REVERT: B 179 MET cc_start: 0.8590 (tpp) cc_final: 0.8104 (tpt) REVERT: B 277 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 404 ILE cc_start: 0.8024 (tt) cc_final: 0.7756 (mt) REVERT: B 492 MET cc_start: 0.7751 (mmm) cc_final: 0.7321 (mtp) REVERT: B 511 TRP cc_start: 0.8032 (m100) cc_final: 0.7618 (m-10) outliers start: 32 outliers final: 25 residues processed: 159 average time/residue: 0.0661 time to fit residues: 15.4523 Evaluate side-chains 154 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 418 HIS B 171 HIS B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121115 restraints weight = 12566.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123518 restraints weight = 8144.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125298 restraints weight = 5853.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126473 restraints weight = 4539.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127365 restraints weight = 3736.193| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9148 Z= 0.108 Angle : 0.585 8.605 12412 Z= 0.281 Chirality : 0.038 0.136 1430 Planarity : 0.004 0.036 1490 Dihedral : 9.568 70.061 1350 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.58 % Allowed : 20.60 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.26), residues: 1076 helix: 0.86 (0.21), residues: 640 sheet: -1.46 (0.56), residues: 74 loop : -2.74 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 651 TYR 0.016 0.001 TYR B 297 PHE 0.008 0.001 PHE B 281 TRP 0.008 0.001 TRP A 583 HIS 0.009 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9146) covalent geometry : angle 0.58418 / 0.28 (12408) SS BOND : bond 0.00732 / 0.37 ( 2) SS BOND : angle 1.48136 / 0.88 ( 4) hydrogen bonds : bond 0.03311 / 2.15 ( 454) hydrogen bonds : angle 3.95062 / 2.71 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.319 Fit side-chains REVERT: A 178 MET cc_start: 0.7926 (mmm) cc_final: 0.7498 (mmm) REVERT: A 405 MET cc_start: 0.8233 (tmm) cc_final: 0.7838 (tmm) REVERT: A 492 MET cc_start: 0.7607 (mmm) cc_final: 0.7233 (mtp) REVERT: A 500 MET cc_start: 0.7019 (mmt) cc_final: 0.6368 (mtm) REVERT: A 511 TRP cc_start: 0.7876 (m100) cc_final: 0.7458 (m-10) REVERT: A 660 TYR cc_start: 0.7978 (t80) cc_final: 0.7549 (t80) REVERT: B 178 MET cc_start: 0.8003 (mmm) cc_final: 0.7372 (mmm) REVERT: B 179 MET cc_start: 0.8600 (tpp) cc_final: 0.8320 (tpt) REVERT: B 277 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 405 MET cc_start: 0.8271 (tmm) cc_final: 0.7821 (tmm) REVERT: B 407 ASP cc_start: 0.8217 (t0) cc_final: 0.7975 (m-30) REVERT: B 492 MET cc_start: 0.7657 (mmm) cc_final: 0.7267 (mtp) REVERT: B 500 MET cc_start: 0.6932 (mmt) cc_final: 0.6311 (mtm) REVERT: B 511 TRP cc_start: 0.7871 (m100) cc_final: 0.7494 (m-10) REVERT: B 660 TYR cc_start: 0.7964 (t80) cc_final: 0.7536 (t80) outliers start: 24 outliers final: 16 residues processed: 159 average time/residue: 0.0643 time to fit residues: 15.5218 Evaluate side-chains 151 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.0570 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 171 HIS A 418 HIS B 164 GLN B 418 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123817 restraints weight = 12539.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126313 restraints weight = 8094.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128068 restraints weight = 5774.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129202 restraints weight = 4470.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129978 restraints weight = 3690.105| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9148 Z= 0.103 Angle : 0.576 7.042 12412 Z= 0.277 Chirality : 0.038 0.149 1430 Planarity : 0.003 0.036 1490 Dihedral : 9.347 66.365 1350 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.93 % Allowed : 21.35 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1076 helix: 1.01 (0.21), residues: 640 sheet: -1.33 (0.57), residues: 74 loop : -2.67 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 651 TYR 0.012 0.001 TYR B 297 PHE 0.013 0.001 PHE A 281 TRP 0.007 0.001 TRP A 583 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9146) covalent geometry : angle 0.57554 / 0.28 (12408) SS BOND : bond 0.00719 / 0.36 ( 2) SS BOND : angle 1.27647 / 0.77 ( 4) hydrogen bonds : bond 0.03114 / 2.04 ( 454) hydrogen bonds : angle 3.87832 / 2.64 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.268 Fit side-chains REVERT: A 405 MET cc_start: 0.8371 (tmm) cc_final: 0.7939 (tmm) REVERT: A 492 MET cc_start: 0.7584 (mmm) cc_final: 0.7204 (mtp) REVERT: A 500 MET cc_start: 0.6943 (mmt) cc_final: 0.6372 (mtm) REVERT: A 511 TRP cc_start: 0.7785 (m100) cc_final: 0.7417 (m-10) REVERT: A 660 TYR cc_start: 0.7946 (t80) cc_final: 0.7547 (t80) REVERT: B 179 MET cc_start: 0.8586 (tpp) cc_final: 0.8311 (tpt) REVERT: B 277 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 405 MET cc_start: 0.8419 (tmm) cc_final: 0.7965 (tmm) REVERT: B 492 MET cc_start: 0.7652 (mmm) cc_final: 0.7247 (mtp) REVERT: B 500 MET cc_start: 0.6879 (mmt) cc_final: 0.6365 (mtm) REVERT: B 511 TRP cc_start: 0.7801 (m100) cc_final: 0.7435 (m-10) REVERT: B 660 TYR cc_start: 0.7918 (t80) cc_final: 0.7514 (t80) outliers start: 18 outliers final: 14 residues processed: 160 average time/residue: 0.0621 time to fit residues: 15.0551 Evaluate side-chains 149 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 418 HIS B 164 GLN B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118824 restraints weight = 12711.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121350 restraints weight = 8160.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123161 restraints weight = 5809.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124429 restraints weight = 4476.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125236 restraints weight = 3652.963| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9148 Z= 0.185 Angle : 0.636 7.277 12412 Z= 0.309 Chirality : 0.042 0.214 1430 Planarity : 0.004 0.037 1490 Dihedral : 9.225 65.132 1350 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.68 % Allowed : 21.57 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1076 helix: 1.00 (0.22), residues: 632 sheet: -1.52 (0.57), residues: 74 loop : -2.52 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 651 TYR 0.010 0.001 TYR A 288 PHE 0.013 0.002 PHE B 281 TRP 0.003 0.001 TRP A 480 HIS 0.009 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 ( 9146) covalent geometry : angle 0.63619 / 0.31 (12408) SS BOND : bond 0.00501 / 0.25 ( 2) SS BOND : angle 1.13157 / 0.68 ( 4) hydrogen bonds : bond 0.03572 / 2.32 ( 454) hydrogen bonds : angle 4.04030 / 2.77 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.226 Fit side-chains REVERT: A 178 MET cc_start: 0.8109 (mmm) cc_final: 0.7439 (mmm) REVERT: A 405 MET cc_start: 0.8464 (tmm) cc_final: 0.7892 (tmm) REVERT: A 407 ASP cc_start: 0.8444 (t0) cc_final: 0.7911 (m-30) REVERT: A 492 MET cc_start: 0.7668 (mmm) cc_final: 0.7276 (mtp) REVERT: A 500 MET cc_start: 0.6961 (mmt) cc_final: 0.6330 (mtm) REVERT: A 511 TRP cc_start: 0.8116 (m100) cc_final: 0.7619 (m-10) REVERT: B 178 MET cc_start: 0.7963 (mmm) cc_final: 0.7422 (mmm) REVERT: B 179 MET cc_start: 0.8612 (tpp) cc_final: 0.8204 (tpt) REVERT: B 303 ASN cc_start: 0.7831 (p0) cc_final: 0.7507 (p0) REVERT: B 405 MET cc_start: 0.8490 (tmm) cc_final: 0.7959 (tmm) REVERT: B 407 ASP cc_start: 0.8299 (t0) cc_final: 0.8077 (m-30) REVERT: B 492 MET cc_start: 0.7700 (mmm) cc_final: 0.7306 (mtp) REVERT: B 500 MET cc_start: 0.6886 (mmt) cc_final: 0.6307 (mtm) REVERT: B 511 TRP cc_start: 0.8091 (m100) cc_final: 0.7602 (m-10) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.0621 time to fit residues: 14.5581 Evaluate side-chains 154 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 418 HIS B 164 GLN B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119949 restraints weight = 12640.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122544 restraints weight = 8062.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124406 restraints weight = 5722.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125718 restraints weight = 4390.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126637 restraints weight = 3570.415| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9148 Z= 0.137 Angle : 0.598 7.642 12412 Z= 0.290 Chirality : 0.040 0.133 1430 Planarity : 0.004 0.036 1490 Dihedral : 8.951 62.529 1350 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.93 % Allowed : 22.21 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.27), residues: 1076 helix: 1.11 (0.22), residues: 630 sheet: -1.43 (0.58), residues: 74 loop : -2.48 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 651 TYR 0.009 0.001 TYR B 297 PHE 0.018 0.001 PHE A 501 TRP 0.005 0.001 TRP A 583 HIS 0.004 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9146) covalent geometry : angle 0.59765 / 0.29 (12408) SS BOND : bond 0.00628 / 0.32 ( 2) SS BOND : angle 1.35027 / 0.82 ( 4) hydrogen bonds : bond 0.03399 / 2.22 ( 454) hydrogen bonds : angle 3.94987 / 2.71 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.306 Fit side-chains REVERT: A 178 MET cc_start: 0.8105 (mmm) cc_final: 0.7452 (mmm) REVERT: A 405 MET cc_start: 0.8430 (tmm) cc_final: 0.7899 (tmm) REVERT: A 407 ASP cc_start: 0.8380 (t0) cc_final: 0.7892 (m-30) REVERT: A 492 MET cc_start: 0.7678 (mmm) cc_final: 0.7295 (mtp) REVERT: A 500 MET cc_start: 0.6913 (mmt) cc_final: 0.6395 (mtm) REVERT: A 511 TRP cc_start: 0.8053 (m100) cc_final: 0.7559 (m-10) REVERT: A 660 TYR cc_start: 0.7960 (t80) cc_final: 0.7545 (t80) REVERT: B 179 MET cc_start: 0.8573 (tpp) cc_final: 0.8129 (tpt) REVERT: B 405 MET cc_start: 0.8461 (tmm) cc_final: 0.7965 (tmm) REVERT: B 407 ASP cc_start: 0.8269 (t0) cc_final: 0.8034 (m-30) REVERT: B 492 MET cc_start: 0.7694 (mmm) cc_final: 0.7287 (mtp) REVERT: B 500 MET cc_start: 0.6880 (mmt) cc_final: 0.6385 (mtm) REVERT: B 511 TRP cc_start: 0.8016 (m100) cc_final: 0.7554 (m-10) REVERT: B 660 TYR cc_start: 0.7974 (t80) cc_final: 0.7564 (t80) outliers start: 18 outliers final: 18 residues processed: 157 average time/residue: 0.0651 time to fit residues: 15.2536 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 0.0060 chunk 81 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 418 HIS B 164 GLN B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135346 restraints weight = 11913.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137397 restraints weight = 7912.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138940 restraints weight = 5796.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139779 restraints weight = 4545.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140559 restraints weight = 3857.628| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9148 Z= 0.114 Angle : 0.589 8.198 12412 Z= 0.284 Chirality : 0.039 0.129 1430 Planarity : 0.004 0.036 1490 Dihedral : 8.775 59.965 1350 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.04 % Allowed : 22.42 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.27), residues: 1076 helix: 1.14 (0.22), residues: 638 sheet: -1.30 (0.58), residues: 74 loop : -2.59 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.010 0.001 TYR B 297 PHE 0.040 0.001 PHE B 522 TRP 0.008 0.002 TRP B 583 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9146) covalent geometry : angle 0.58816 / 0.28 (12408) SS BOND : bond 0.00666 / 0.33 ( 2) SS BOND : angle 1.27482 / 0.77 ( 4) hydrogen bonds : bond 0.03250 / 2.12 ( 454) hydrogen bonds : angle 3.91329 / 2.67 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.300 Fit side-chains REVERT: A 178 MET cc_start: 0.8094 (mmm) cc_final: 0.7466 (mmm) REVERT: A 405 MET cc_start: 0.8394 (tmm) cc_final: 0.7876 (tmm) REVERT: A 407 ASP cc_start: 0.8357 (t0) cc_final: 0.7868 (m-30) REVERT: A 492 MET cc_start: 0.7643 (mmm) cc_final: 0.7253 (mtp) REVERT: A 500 MET cc_start: 0.6827 (mmt) cc_final: 0.6437 (mtm) REVERT: A 511 TRP cc_start: 0.7931 (m100) cc_final: 0.7456 (m-10) REVERT: A 660 TYR cc_start: 0.7933 (t80) cc_final: 0.7519 (t80) REVERT: B 178 MET cc_start: 0.7986 (mmm) cc_final: 0.7425 (mmm) REVERT: B 179 MET cc_start: 0.8551 (tpp) cc_final: 0.8239 (tpt) REVERT: B 405 MET cc_start: 0.8443 (tmm) cc_final: 0.7946 (tmm) REVERT: B 492 MET cc_start: 0.7685 (mmm) cc_final: 0.7278 (mtp) REVERT: B 500 MET cc_start: 0.6791 (mmt) cc_final: 0.6405 (mtm) REVERT: B 511 TRP cc_start: 0.7934 (m100) cc_final: 0.7465 (m-10) REVERT: B 660 TYR cc_start: 0.7945 (t80) cc_final: 0.7538 (t80) outliers start: 19 outliers final: 17 residues processed: 165 average time/residue: 0.0593 time to fit residues: 14.7007 Evaluate side-chains 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 418 HIS B 164 GLN B 418 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122557 restraints weight = 12377.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124837 restraints weight = 8018.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126642 restraints weight = 5778.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127737 restraints weight = 4481.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128673 restraints weight = 3702.262| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9148 Z= 0.112 Angle : 0.589 8.021 12412 Z= 0.283 Chirality : 0.040 0.269 1430 Planarity : 0.003 0.037 1490 Dihedral : 8.625 59.255 1350 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.93 % Allowed : 22.75 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1076 helix: 1.14 (0.21), residues: 642 sheet: -1.25 (0.58), residues: 74 loop : -2.52 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 651 TYR 0.009 0.001 TYR B 297 PHE 0.036 0.001 PHE B 522 TRP 0.008 0.001 TRP B 583 HIS 0.005 0.001 HIS B 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9146) covalent geometry : angle 0.58876 / 0.28 (12408) SS BOND : bond 0.00641 / 0.32 ( 2) SS BOND : angle 1.19663 / 0.72 ( 4) hydrogen bonds : bond 0.03195 / 2.09 ( 454) hydrogen bonds : angle 3.87777 / 2.64 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.59 seconds wall clock time: 21 minutes 30.67 seconds (1290.67 seconds total)