Starting phenix.real_space_refine on Thu Jul 2 18:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bi0_16075/07_2026/8bi0_16075.map" } resolution = 3.2 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= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 6004 2.51 5 N 1478 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 9198 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4445 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 4 Chain: "B" Number of atoms: 4445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4445 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 20, 'TRANS': 550} Chain breaks: 4 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' MG': 1, 'ATP': 1, 'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {' MG': 1, 'ATP': 1, 'CLR': 2, 'PLC': 1, 'R1H': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9198 At special positions: 0 Unit cell: (95.7, 91.74, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 8 15.00 Mg 2 11.99 O 1648 8.00 N 1478 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 0.73 Conformation dependent library (CDL) restraints added in 247.0 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.663A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.666A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.619A pdb=" N ALA A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.710A pdb=" N PHE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.517A pdb=" N GLN A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 413 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 440 through 451 removed outlier: 4.412A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.518A pdb=" N TYR A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 3.670A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.640A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 533 through 551 removed outlier: 3.623A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.132A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.728A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.819A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.662A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.666A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.619A pdb=" N ALA B 280 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.710A pdb=" N PHE B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.590A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.518A pdb=" N GLN B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 413 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 440 through 451 removed outlier: 4.411A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.518A pdb=" N TYR B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.670A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.640A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 533 through 551 removed outlier: 3.623A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.132A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.728A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.820A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 71 removed outlier: 6.808A pdb=" N TYR A 44 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER A 65 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 42 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 67 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS A 40 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY A 69 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER A 38 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 5.987A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 71 removed outlier: 6.809A pdb=" N TYR B 44 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER B 65 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE B 42 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 67 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS B 40 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY B 69 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER B 38 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124 removed outlier: 5.986A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1506 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: 1.21 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1399 1.31 - 1.44: 2535 1.44 - 1.57: 5345 1.57 - 1.70: 28 1.70 - 1.83: 94 Bond restraints: 9401 Sorted by residual: bond pdb=" C13 R1H B1505 " pdb=" N08 R1H B1505 " ideal model delta sigma weight residual 1.448 1.292 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP B1501 " pdb=" C5 ATP B1501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C5 ATP B1501 " pdb=" C6 ATP B1501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 12618 3.66 - 7.32: 100 7.32 - 10.98: 20 10.98 - 14.64: 0 14.64 - 18.30: 6 Bond angle restraints: 12744 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 121.63 18.24 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 119.53 17.30 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.57 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" C5 ATP B1501 " pdb=" C4 ATP B1501 " pdb=" N3 ATP B1501 " ideal model delta sigma weight residual 126.80 119.16 7.64 1.00e+00 1.00e+00 5.84e+01 ... (remaining 12739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 5341 24.56 - 49.11: 142 49.11 - 73.67: 20 73.67 - 98.23: 2 98.23 - 122.78: 4 Dihedral angle restraints: 5509 sinusoidal: 2217 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 140.59 -47.59 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" SG CYS A 603 " pdb=" CB CYS B 603 " pdb=" SG CYS B 603 " pdb=" CA CYS B 603 " ideal model delta sinusoidal sigma weight residual 79.00 4.00 75.00 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" C13 R1H B1505 " pdb=" C14 R1H B1505 " pdb=" C15 R1H B1505 " pdb=" C16 R1H B1505 " ideal model delta sinusoidal sigma weight residual 160.69 37.91 122.78 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1339 0.073 - 0.147: 103 0.147 - 0.220: 14 0.220 - 0.294: 6 0.294 - 0.367: 4 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C17 CLR B1502 " pdb=" C13 CLR B1502 " pdb=" C16 CLR B1502 " pdb=" C20 CLR B1502 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 CLR A1502 " pdb=" C13 CLR A1502 " pdb=" C16 CLR A1502 " pdb=" C20 CLR A1502 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C17 CLR B1503 " pdb=" C13 CLR B1503 " pdb=" C16 CLR B1503 " pdb=" C20 CLR B1503 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1463 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 212 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 212 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 500 " -0.018 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO A 501 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " -0.015 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 5 1.99 - 2.71: 289 2.71 - 3.44: 13643 3.44 - 4.17: 20227 4.17 - 4.90: 39466 Nonbonded interactions: 73630 Sorted by model distance: nonbonded pdb=" O1G ATP B1501 " pdb="MG MG B1506 " model vdw 1.257 2.170 nonbonded pdb=" O1G ATP A1501 " pdb="MG MG A1505 " model vdw 1.521 2.170 nonbonded pdb=" NE2 GLN A 126 " pdb="MG MG A1505 " model vdw 1.897 2.250 nonbonded pdb=" OE1 GLN A 126 " pdb="MG MG A1505 " model vdw 1.918 2.170 nonbonded pdb=" O1B ATP B1501 " pdb="MG MG B1506 " model vdw 1.956 2.170 ... (remaining 73625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 1504) selection = (chain 'B' and resid 34 through 1504) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.156 9404 Z= 0.404 Angle : 0.890 18.295 12750 Z= 0.524 Chirality : 0.049 0.367 1466 Planarity : 0.003 0.035 1538 Dihedral : 11.899 122.782 3384 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.35 % Rotamer: Outliers : 0.20 % Allowed : 4.20 % Favored : 95.59 % 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: 0.83 (0.25), residues: 1122 helix: 1.55 (0.20), residues: 654 sheet: -0.68 (0.62), residues: 68 loop : -0.87 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 482 TYR 0.014 0.001 TYR A 463 PHE 0.011 0.001 PHE A 39 TRP 0.011 0.002 TRP B 564 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.40 ( 9401) covalent geometry : angle 0.88896 / 0.52 (12744) SS BOND : bond 0.00176 / 0.10 ( 3) SS BOND : angle 2.28814 / 1.40 ( 6) hydrogen bonds : bond 0.18618 / 12.44 ( 516) hydrogen bonds : angle 6.11910 / 4.39 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.265 Fit side-chains REVERT: B 585 GLU cc_start: 0.7706 (tp30) cc_final: 0.7476 (tp30) outliers start: 2 outliers final: 0 residues processed: 158 average time/residue: 0.1067 time to fit residues: 22.9696 Evaluate side-chains 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN A 299 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092823 restraints weight = 15787.103| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.22 r_work: 0.3127 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9404 Z= 0.143 Angle : 0.556 8.298 12750 Z= 0.294 Chirality : 0.040 0.136 1466 Planarity : 0.003 0.026 1538 Dihedral : 8.460 98.343 1334 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.33 % Allowed : 9.43 % Favored : 89.24 % 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: 1.57 (0.26), residues: 1122 helix: 2.23 (0.20), residues: 664 sheet: -0.25 (0.69), residues: 50 loop : -0.84 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.015 0.001 TYR B 605 PHE 0.020 0.001 PHE A 293 TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9401) covalent geometry : angle 0.55473 / 0.29 (12744) SS BOND : bond 0.00880 / 0.52 ( 3) SS BOND : angle 2.00279 / 1.14 ( 6) hydrogen bonds : bond 0.05187 / 3.41 ( 516) hydrogen bonds : angle 4.25271 / 3.07 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.383 Fit side-chains REVERT: A 477 ASP cc_start: 0.8124 (t0) cc_final: 0.7808 (t0) REVERT: B 494 TYR cc_start: 0.8806 (t80) cc_final: 0.8591 (t80) REVERT: B 585 GLU cc_start: 0.8742 (tp30) cc_final: 0.8421 (tp30) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.0878 time to fit residues: 12.3887 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086620 restraints weight = 16068.774| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.25 r_work: 0.3034 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9404 Z= 0.163 Angle : 0.533 6.860 12750 Z= 0.277 Chirality : 0.040 0.138 1466 Planarity : 0.003 0.032 1538 Dihedral : 7.782 88.988 1334 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.74 % Allowed : 10.76 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.26), residues: 1122 helix: 2.37 (0.20), residues: 670 sheet: 0.08 (0.69), residues: 50 loop : -0.93 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.012 0.001 TYR A 459 PHE 0.018 0.001 PHE A 293 TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9401) covalent geometry : angle 0.53282 / 0.28 (12744) SS BOND : bond 0.00285 / 0.17 ( 3) SS BOND : angle 0.92218 / 0.48 ( 6) hydrogen bonds : bond 0.04595 / 2.98 ( 516) hydrogen bonds : angle 3.89838 / 2.80 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.286 Fit side-chains REVERT: B 585 GLU cc_start: 0.8871 (tp30) cc_final: 0.8660 (tp30) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.0663 time to fit residues: 9.8505 Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085991 restraints weight = 16338.130| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.29 r_work: 0.3021 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9404 Z= 0.163 Angle : 0.510 6.849 12750 Z= 0.265 Chirality : 0.040 0.138 1466 Planarity : 0.003 0.032 1538 Dihedral : 7.492 88.663 1334 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.95 % Allowed : 11.48 % Favored : 86.58 % 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: 1.78 (0.26), residues: 1122 helix: 2.44 (0.20), residues: 670 sheet: 0.25 (0.69), residues: 50 loop : -0.95 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.011 0.001 TYR B 336 PHE 0.018 0.001 PHE A 293 TRP 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 9401) covalent geometry : angle 0.50952 / 0.27 (12744) SS BOND : bond 0.00252 / 0.15 ( 3) SS BOND : angle 0.70704 / 0.37 ( 6) hydrogen bonds : bond 0.04555 / 2.96 ( 516) hydrogen bonds : angle 3.83389 / 2.77 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.424 Fit side-chains REVERT: A 161 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 299 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8919 (t0) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 0.0677 time to fit residues: 8.5412 Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088371 restraints weight = 16150.158| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.28 r_work: 0.3066 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9404 Z= 0.095 Angle : 0.447 5.536 12750 Z= 0.234 Chirality : 0.037 0.138 1466 Planarity : 0.003 0.031 1538 Dihedral : 7.020 85.795 1334 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.74 % Allowed : 12.19 % Favored : 86.07 % 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: 2.04 (0.26), residues: 1122 helix: 2.68 (0.20), residues: 670 sheet: 0.55 (0.70), residues: 50 loop : -0.93 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 263 TYR 0.009 0.001 TYR B 459 PHE 0.017 0.001 PHE B 293 TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 9401) covalent geometry : angle 0.44647 / 0.23 (12744) SS BOND : bond 0.00280 / 0.16 ( 3) SS BOND : angle 0.64240 / 0.38 ( 6) hydrogen bonds : bond 0.03519 / 2.29 ( 516) hydrogen bonds : angle 3.60261 / 2.60 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.230 Fit side-chains REVERT: A 299 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8883 (t0) REVERT: A 515 MET cc_start: 0.8909 (mmm) cc_final: 0.8692 (mmp) REVERT: A 525 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8770 (mp) REVERT: B 265 MET cc_start: 0.8763 (mmt) cc_final: 0.8409 (mmt) REVERT: B 489 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8321 (m-80) outliers start: 17 outliers final: 7 residues processed: 90 average time/residue: 0.0705 time to fit residues: 9.9005 Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.0010 chunk 81 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085682 restraints weight = 16446.076| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.29 r_work: 0.3016 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9404 Z= 0.146 Angle : 0.486 6.222 12750 Z= 0.253 Chirality : 0.039 0.139 1466 Planarity : 0.003 0.036 1538 Dihedral : 7.109 86.076 1334 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 12.50 % Favored : 85.35 % 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: 1.99 (0.26), residues: 1122 helix: 2.60 (0.20), residues: 670 sheet: 0.73 (0.70), residues: 50 loop : -0.90 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 263 TYR 0.009 0.001 TYR A 459 PHE 0.016 0.001 PHE A 293 TRP 0.010 0.001 TRP B 379 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9401) covalent geometry : angle 0.48601 / 0.25 (12744) SS BOND : bond 0.00218 / 0.12 ( 3) SS BOND : angle 0.74767 / 0.44 ( 6) hydrogen bonds : bond 0.04148 / 2.68 ( 516) hydrogen bonds : angle 3.65545 / 2.63 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.290 Fit side-chains REVERT: A 299 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8916 (t0) REVERT: A 525 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8784 (mp) REVERT: B 131 MET cc_start: 0.9187 (mmt) cc_final: 0.8928 (tpt) REVERT: B 489 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8370 (m-80) outliers start: 21 outliers final: 13 residues processed: 84 average time/residue: 0.0699 time to fit residues: 9.2491 Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 608 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085975 restraints weight = 16352.748| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.29 r_work: 0.3029 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9404 Z= 0.116 Angle : 0.454 5.815 12750 Z= 0.236 Chirality : 0.037 0.139 1466 Planarity : 0.003 0.039 1538 Dihedral : 6.960 83.920 1334 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.05 % Allowed : 13.01 % Favored : 84.94 % 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: 2.07 (0.26), residues: 1122 helix: 2.66 (0.20), residues: 670 sheet: 0.89 (0.72), residues: 50 loop : -0.88 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 263 TYR 0.008 0.001 TYR B 459 PHE 0.015 0.001 PHE B 293 TRP 0.010 0.001 TRP B 379 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9401) covalent geometry : angle 0.45435 / 0.24 (12744) SS BOND : bond 0.00204 / 0.12 ( 3) SS BOND : angle 0.62591 / 0.36 ( 6) hydrogen bonds : bond 0.03806 / 2.46 ( 516) hydrogen bonds : angle 3.59150 / 2.58 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.353 Fit side-chains REVERT: A 152 MET cc_start: 0.8478 (mtp) cc_final: 0.8009 (ttm) REVERT: A 299 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8917 (t0) REVERT: A 525 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8769 (mp) REVERT: B 489 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8374 (m-80) outliers start: 20 outliers final: 14 residues processed: 83 average time/residue: 0.0695 time to fit residues: 9.0837 Evaluate side-chains 81 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082820 restraints weight = 16386.455| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.27 r_work: 0.2978 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9404 Z= 0.204 Angle : 0.531 7.092 12750 Z= 0.275 Chirality : 0.040 0.141 1466 Planarity : 0.003 0.044 1538 Dihedral : 7.283 84.969 1334 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.36 % Allowed : 12.81 % Favored : 84.84 % 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: 1.85 (0.26), residues: 1122 helix: 2.46 (0.20), residues: 670 sheet: 0.90 (0.72), residues: 50 loop : -0.95 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.013 0.001 TYR A 463 PHE 0.017 0.001 PHE A 293 TRP 0.008 0.001 TRP B 379 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 ( 9401) covalent geometry : angle 0.52976 / 0.27 (12744) SS BOND : bond 0.00210 / 0.12 ( 3) SS BOND : angle 1.87379 / 1.14 ( 6) hydrogen bonds : bond 0.04783 / 3.08 ( 516) hydrogen bonds : angle 3.76412 / 2.70 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.259 Fit side-chains REVERT: A 299 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8940 (t0) REVERT: A 525 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8775 (mp) REVERT: B 246 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8240 (mtm180) REVERT: B 489 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8376 (m-80) outliers start: 23 outliers final: 16 residues processed: 85 average time/residue: 0.0729 time to fit residues: 9.3717 Evaluate side-chains 84 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086220 restraints weight = 16329.180| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.29 r_work: 0.3024 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9404 Z= 0.105 Angle : 0.460 5.827 12750 Z= 0.240 Chirality : 0.037 0.141 1466 Planarity : 0.003 0.043 1538 Dihedral : 6.967 82.315 1334 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.74 % Allowed : 13.52 % Favored : 84.73 % 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: 2.02 (0.26), residues: 1122 helix: 2.60 (0.20), residues: 672 sheet: 1.03 (0.73), residues: 50 loop : -0.91 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.009 0.001 TYR B 459 PHE 0.015 0.001 PHE B 293 TRP 0.011 0.001 TRP B 379 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9401) covalent geometry : angle 0.45873 / 0.24 (12744) SS BOND : bond 0.00168 / 0.10 ( 3) SS BOND : angle 1.56158 / 0.95 ( 6) hydrogen bonds : bond 0.03811 / 2.45 ( 516) hydrogen bonds : angle 3.61818 / 2.61 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.203 Fit side-chains REVERT: A 299 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8932 (t0) REVERT: A 525 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 489 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8371 (m-80) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.0664 time to fit residues: 8.2506 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 0.0020 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084721 restraints weight = 16605.969| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.29 r_work: 0.2997 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9404 Z= 0.150 Angle : 0.487 6.253 12750 Z= 0.252 Chirality : 0.039 0.141 1466 Planarity : 0.003 0.044 1538 Dihedral : 7.020 83.934 1334 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.05 % Allowed : 13.63 % Favored : 84.32 % 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: 1.95 (0.26), residues: 1122 helix: 2.54 (0.20), residues: 672 sheet: 1.06 (0.73), residues: 50 loop : -0.92 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.011 0.001 TYR B 336 PHE 0.015 0.001 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9401) covalent geometry : angle 0.48529 / 0.25 (12744) SS BOND : bond 0.00301 / 0.18 ( 3) SS BOND : angle 1.80483 / 1.01 ( 6) hydrogen bonds : bond 0.04162 / 2.68 ( 516) hydrogen bonds : angle 3.65687 / 2.63 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.326 Fit side-chains REVERT: A 299 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8933 (t0) REVERT: A 525 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8751 (mp) REVERT: B 246 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8185 (mtm180) REVERT: B 489 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8395 (m-80) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.0751 time to fit residues: 9.0635 Evaluate side-chains 80 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 ASN B 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084689 restraints weight = 16314.843| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.28 r_work: 0.2997 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9404 Z= 0.147 Angle : 0.482 6.329 12750 Z= 0.250 Chirality : 0.038 0.141 1466 Planarity : 0.003 0.043 1538 Dihedral : 7.020 85.518 1334 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.25 % Allowed : 13.42 % Favored : 84.32 % 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: 1.95 (0.26), residues: 1122 helix: 2.53 (0.20), residues: 672 sheet: 1.08 (0.74), residues: 50 loop : -0.90 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.010 0.001 TYR B 336 PHE 0.015 0.001 PHE A 293 TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9401) covalent geometry : angle 0.48124 / 0.25 (12744) SS BOND : bond 0.00205 / 0.12 ( 3) SS BOND : angle 1.47682 / 0.85 ( 6) hydrogen bonds : bond 0.04180 / 2.69 ( 516) hydrogen bonds : angle 3.65959 / 2.63 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.34 seconds wall clock time: 40 minutes 18.20 seconds (2418.20 seconds total)