Starting phenix.real_space_refine on Fri Jul 3 04:15:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.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/7tai_25775/07_2026/7tai_25775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.map" model { file = "/net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tai_25775/07_2026/7tai_25775.cif" } 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= 0.006 sd= 0.082 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 Fe 3 7.16 5 P 18 5.49 5 S 30 5.16 5 C 7350 2.51 5 N 1812 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 11109 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3454 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'CLR': 2, 'FAD': 1, 'HEM': 1, 'LBN': 1, 'NAP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: A, C Time building chain proxies: 2.44, per 1000 atoms: 0.22 Number of scatterers: 11109 At special positions: 0 Unit cell: (95.141, 93.003, 101.555, 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) Fe 3 26.01 S 30 16.00 P 18 15.00 O 1896 8.00 N 1812 7.00 C 7350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 405.8 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 64.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.818A pdb=" N LEU B 83 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 94 through 102 removed outlier: 4.709A pdb=" N THR B 99 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 212 through 235 Processing helix chain 'B' and resid 235 through 240 removed outlier: 4.107A pdb=" N ALA B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 258 through 285 removed outlier: 3.624A pdb=" N ALA B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 301 through 323 Processing helix chain 'B' and resid 351 through 378 Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 387 through 419 removed outlier: 3.897A pdb=" N TYR B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 419 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 449 removed outlier: 4.118A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 435 " --> pdb=" O ASN B 431 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.652A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.818A pdb=" N LEU A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 94 through 102 removed outlier: 4.709A pdb=" N THR A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 212 through 235 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.107A pdb=" N ALA A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.625A pdb=" N ALA A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 301 through 323 Processing helix chain 'A' and resid 351 through 378 Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 387 through 419 removed outlier: 3.897A pdb=" N TYR A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE A 419 " --> pdb=" O TRP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 449 removed outlier: 4.118A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.651A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.817A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 94 through 102 removed outlier: 4.709A pdb=" N THR C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 197 through 204 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 212 through 235 Processing helix chain 'C' and resid 235 through 240 removed outlier: 4.107A pdb=" N ALA C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 258 through 285 removed outlier: 3.625A pdb=" N ALA C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 301 through 323 Processing helix chain 'C' and resid 351 through 378 Processing helix chain 'C' and resid 379 through 385 Processing helix chain 'C' and resid 387 through 419 removed outlier: 3.897A pdb=" N TYR C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 419 " --> pdb=" O TRP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 449 removed outlier: 4.118A pdb=" N LEU C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 451 through 463 removed outlier: 3.651A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 77 removed outlier: 7.081A pdb=" N VAL B 56 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR B 77 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 58 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 33 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 35 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 88 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 113 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 77 removed outlier: 7.081A pdb=" N VAL A 56 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR A 77 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE A 58 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 33 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 35 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 88 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 113 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 77 removed outlier: 7.081A pdb=" N VAL C 56 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR C 77 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 58 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 33 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 35 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE C 88 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 113 " --> pdb=" O VAL C 143 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1701 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: 1.65 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3473 1.37 - 1.54: 7830 1.54 - 1.71: 88 1.71 - 1.88: 45 1.88 - 2.05: 12 Bond restraints: 11448 Sorted by residual: bond pdb=" O2B NAP B 503 " pdb=" P2B NAP B 503 " ideal model delta sigma weight residual 1.736 1.594 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O2B NAP A 503 " pdb=" P2B NAP A 503 " ideal model delta sigma weight residual 1.736 1.594 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" O2B NAP C 503 " pdb=" P2B NAP C 503 " ideal model delta sigma weight residual 1.736 1.595 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " ideal model delta sigma weight residual 1.660 1.590 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.590 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 11443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 15232 2.24 - 4.47: 341 4.47 - 6.71: 70 6.71 - 8.94: 17 8.94 - 11.18: 6 Bond angle restraints: 15666 Sorted by residual: angle pdb=" C2B NAP C 503 " pdb=" O2B NAP C 503 " pdb=" P2B NAP C 503 " ideal model delta sigma weight residual 117.19 128.37 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C2B NAP B 503 " pdb=" O2B NAP B 503 " pdb=" P2B NAP B 503 " ideal model delta sigma weight residual 117.19 128.35 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C2B NAP A 503 " pdb=" O2B NAP A 503 " pdb=" P2B NAP A 503 " ideal model delta sigma weight residual 117.19 128.34 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1 LBN C 504 " pdb=" P1 LBN C 504 " pdb=" O2 LBN C 504 " ideal model delta sigma weight residual 93.45 104.06 -10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN B 504 " pdb=" P1 LBN B 504 " pdb=" O2 LBN B 504 " ideal model delta sigma weight residual 93.45 104.06 -10.61 3.00e+00 1.11e-01 1.25e+01 ... (remaining 15661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 6207 27.64 - 55.27: 276 55.27 - 82.91: 27 82.91 - 110.54: 9 110.54 - 138.18: 12 Dihedral angle restraints: 6531 sinusoidal: 2772 harmonic: 3759 Sorted by residual: dihedral pdb=" CA ILE B 252 " pdb=" C ILE B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta harmonic sigma weight residual 180.00 147.76 32.24 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA ILE A 252 " pdb=" C ILE A 252 " pdb=" N GLU A 253 " pdb=" CA GLU A 253 " ideal model delta harmonic sigma weight residual 180.00 147.77 32.23 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ILE C 252 " pdb=" C ILE C 252 " pdb=" N GLU C 253 " pdb=" CA GLU C 253 " ideal model delta harmonic sigma weight residual 180.00 147.79 32.21 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 6528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1349 0.053 - 0.106: 299 0.106 - 0.159: 71 0.159 - 0.211: 9 0.211 - 0.264: 9 Chirality restraints: 1737 Sorted by residual: chirality pdb=" C2 LBN C 504 " pdb=" C1 LBN C 504 " pdb=" C3 LBN C 504 " pdb=" O7 LBN C 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2 LBN B 504 " pdb=" C1 LBN B 504 " pdb=" C3 LBN B 504 " pdb=" O7 LBN B 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2 LBN A 504 " pdb=" C1 LBN A 504 " pdb=" C3 LBN A 504 " pdb=" O7 LBN A 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1734 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD A 501 " -0.013 2.00e-02 2.50e+03 1.71e-02 1.39e+01 pdb=" C10 FAD A 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 FAD A 501 " 0.003 2.00e-02 2.50e+03 pdb=" C4 FAD A 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4X FAD A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5X FAD A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FAD A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FAD A 501 " 0.006 2.00e-02 2.50e+03 pdb=" C7M FAD A 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 FAD A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C8M FAD A 501 " -0.043 2.00e-02 2.50e+03 pdb=" C9 FAD A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C9A FAD A 501 " 0.010 2.00e-02 2.50e+03 pdb=" N1 FAD A 501 " 0.027 2.00e-02 2.50e+03 pdb=" N10 FAD A 501 " 0.013 2.00e-02 2.50e+03 pdb=" N3 FAD A 501 " -0.015 2.00e-02 2.50e+03 pdb=" N5 FAD A 501 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FAD A 501 " -0.013 2.00e-02 2.50e+03 pdb=" O4 FAD A 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD B 501 " -0.013 2.00e-02 2.50e+03 1.70e-02 1.37e+01 pdb=" C10 FAD B 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 FAD B 501 " 0.004 2.00e-02 2.50e+03 pdb=" C4 FAD B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4X FAD B 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5X FAD B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FAD B 501 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FAD B 501 " 0.006 2.00e-02 2.50e+03 pdb=" C7M FAD B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 FAD B 501 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FAD B 501 " -0.043 2.00e-02 2.50e+03 pdb=" C9 FAD B 501 " -0.000 2.00e-02 2.50e+03 pdb=" C9A FAD B 501 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FAD B 501 " 0.027 2.00e-02 2.50e+03 pdb=" N10 FAD B 501 " 0.013 2.00e-02 2.50e+03 pdb=" N3 FAD B 501 " -0.015 2.00e-02 2.50e+03 pdb=" N5 FAD B 501 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FAD B 501 " -0.013 2.00e-02 2.50e+03 pdb=" O4 FAD B 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 501 " 0.013 2.00e-02 2.50e+03 1.69e-02 1.36e+01 pdb=" C10 FAD C 501 " -0.020 2.00e-02 2.50e+03 pdb=" C2 FAD C 501 " -0.003 2.00e-02 2.50e+03 pdb=" C4 FAD C 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4X FAD C 501 " -0.008 2.00e-02 2.50e+03 pdb=" C5X FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" C6 FAD C 501 " -0.015 2.00e-02 2.50e+03 pdb=" C7 FAD C 501 " -0.007 2.00e-02 2.50e+03 pdb=" C7M FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C8 FAD C 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8M FAD C 501 " 0.043 2.00e-02 2.50e+03 pdb=" C9 FAD C 501 " 0.000 2.00e-02 2.50e+03 pdb=" C9A FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" N1 FAD C 501 " -0.027 2.00e-02 2.50e+03 pdb=" N10 FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" N3 FAD C 501 " 0.015 2.00e-02 2.50e+03 pdb=" N5 FAD C 501 " -0.008 2.00e-02 2.50e+03 pdb=" O2 FAD C 501 " 0.012 2.00e-02 2.50e+03 pdb=" O4 FAD C 501 " 0.030 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 153 2.65 - 3.21: 10307 3.21 - 3.77: 17338 3.77 - 4.34: 24649 4.34 - 4.90: 40059 Nonbonded interactions: 92506 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD1 ASP B 115 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR C 98 " pdb=" OD1 ASP C 115 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OD1 ASP A 115 " model vdw 2.087 3.040 nonbonded pdb=" OG SER B 381 " pdb=" OG SER A 381 " model vdw 2.120 3.040 nonbonded pdb=" OG SER A 381 " pdb=" OG SER C 381 " model vdw 2.126 3.040 ... (remaining 92501 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.090 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.009 0.361 11454 Z= 0.307 Angle : 0.857 11.179 15666 Z= 0.427 Chirality : 0.050 0.264 1737 Planarity : 0.006 0.062 1827 Dihedral : 16.763 138.178 4101 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 0.62 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.97 (0.25), residues: 1260 helix: 1.18 (0.19), residues: 747 sheet: 0.24 (0.55), residues: 108 loop : -0.08 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 456 TYR 0.023 0.002 TYR B 271 PHE 0.021 0.002 PHE A 69 TRP 0.011 0.001 TRP C 355 HIS 0.005 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 (11448) covalent geometry : angle 0.85703 / 0.43 (15666) hydrogen bonds : bond 0.11828 / 8.23 ( 582) hydrogen bonds : angle 5.94906 / 4.25 ( 1701) Misc. bond : bond 0.25464 / 15.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.393 Fit side-chains REVERT: B 65 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 415 TRP cc_start: 0.6647 (t60) cc_final: 0.6210 (t60) REVERT: B 463 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7686 (ttpt) REVERT: A 325 MET cc_start: 0.5738 (mmt) cc_final: 0.3469 (ptp) REVERT: A 415 TRP cc_start: 0.6482 (t60) cc_final: 0.6104 (t60) REVERT: C 80 GLU cc_start: 0.7891 (mp0) cc_final: 0.7661 (mp0) REVERT: C 325 MET cc_start: 0.5514 (mmt) cc_final: 0.4311 (ptm) outliers start: 12 outliers final: 1 residues processed: 110 average time/residue: 0.1081 time to fit residues: 16.7493 Evaluate side-chains 86 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 463 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 HIS A 72 HIS C 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118782 restraints weight = 15314.146| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.91 r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11454 Z= 0.140 Angle : 0.590 6.153 15666 Z= 0.296 Chirality : 0.043 0.198 1737 Planarity : 0.006 0.059 1827 Dihedral : 15.540 128.571 1672 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.71 % Allowed : 5.92 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1260 helix: 1.57 (0.19), residues: 747 sheet: 0.28 (0.51), residues: 123 loop : -0.50 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 456 TYR 0.037 0.002 TYR C 360 PHE 0.019 0.001 PHE A 65 TRP 0.019 0.001 TRP A 355 HIS 0.005 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11448) covalent geometry : angle 0.59016 / 0.30 (15666) hydrogen bonds : bond 0.04732 / 3.36 ( 582) hydrogen bonds : angle 4.98791 / 3.51 ( 1701) Misc. bond : bond 0.03178 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.324 Fit side-chains REVERT: B 65 PHE cc_start: 0.7705 (t80) cc_final: 0.7453 (t80) REVERT: B 81 ASP cc_start: 0.8499 (t0) cc_final: 0.8272 (t0) REVERT: A 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8347 (t0) REVERT: C 80 GLU cc_start: 0.8152 (mp0) cc_final: 0.7860 (mp0) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.0765 time to fit residues: 10.9928 Evaluate side-chains 83 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 0.0000 chunk 119 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN C 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.153503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122934 restraints weight = 15420.037| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.92 r_work: 0.3416 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11454 Z= 0.108 Angle : 0.523 5.060 15666 Z= 0.260 Chirality : 0.042 0.166 1737 Planarity : 0.005 0.057 1827 Dihedral : 14.260 126.444 1662 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.88 % Allowed : 8.58 % Favored : 90.54 % 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: 1.75 (0.25), residues: 1260 helix: 2.07 (0.20), residues: 729 sheet: 0.37 (0.48), residues: 141 loop : -0.23 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 460 TYR 0.030 0.002 TYR C 360 PHE 0.012 0.001 PHE A 65 TRP 0.026 0.001 TRP A 355 HIS 0.002 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (11448) covalent geometry : angle 0.52292 / 0.26 (15666) hydrogen bonds : bond 0.03961 / 2.79 ( 582) hydrogen bonds : angle 4.70168 / 3.29 ( 1701) Misc. bond : bond 0.04099 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.282 Fit side-chains REVERT: B 65 PHE cc_start: 0.7800 (t80) cc_final: 0.7449 (t80) REVERT: B 81 ASP cc_start: 0.8694 (t0) cc_final: 0.8336 (t0) REVERT: A 81 ASP cc_start: 0.8758 (t0) cc_final: 0.8368 (t0) REVERT: A 325 MET cc_start: 0.5560 (mmt) cc_final: 0.3337 (ptp) REVERT: A 417 ARG cc_start: 0.7276 (mtp85) cc_final: 0.6945 (mtp-110) REVERT: C 80 GLU cc_start: 0.8044 (mp0) cc_final: 0.7674 (mp0) REVERT: C 81 ASP cc_start: 0.8703 (t0) cc_final: 0.8447 (t0) REVERT: C 325 MET cc_start: 0.5843 (mmt) cc_final: 0.4520 (ptm) outliers start: 10 outliers final: 6 residues processed: 114 average time/residue: 0.0773 time to fit residues: 13.2111 Evaluate side-chains 93 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120765 restraints weight = 15513.181| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.92 r_work: 0.3380 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11454 Z= 0.122 Angle : 0.536 5.386 15666 Z= 0.266 Chirality : 0.042 0.142 1737 Planarity : 0.005 0.057 1827 Dihedral : 14.173 125.644 1662 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.41 % Allowed : 10.26 % Favored : 88.33 % 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 (0.25), residues: 1260 helix: 1.99 (0.20), residues: 747 sheet: 0.53 (0.53), residues: 123 loop : -0.35 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 417 TYR 0.026 0.002 TYR C 427 PHE 0.008 0.001 PHE A 65 TRP 0.021 0.001 TRP C 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11448) covalent geometry : angle 0.53620 / 0.27 (15666) hydrogen bonds : bond 0.04034 / 2.86 ( 582) hydrogen bonds : angle 4.70438 / 3.28 ( 1701) Misc. bond : bond 0.05519 / 3.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.285 Fit side-chains REVERT: B 65 PHE cc_start: 0.7779 (t80) cc_final: 0.7473 (t80) REVERT: B 81 ASP cc_start: 0.8749 (t0) cc_final: 0.8357 (t0) REVERT: A 81 ASP cc_start: 0.8753 (t0) cc_final: 0.8320 (t0) REVERT: A 325 MET cc_start: 0.5431 (mmt) cc_final: 0.3024 (ptp) REVERT: A 417 ARG cc_start: 0.7353 (mtp85) cc_final: 0.7011 (mtp-110) REVERT: C 80 GLU cc_start: 0.8075 (mp0) cc_final: 0.7700 (mp0) REVERT: C 81 ASP cc_start: 0.8749 (t0) cc_final: 0.8374 (t0) REVERT: C 325 MET cc_start: 0.5612 (mmt) cc_final: 0.4266 (ptm) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.0820 time to fit residues: 12.4948 Evaluate side-chains 100 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 170 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120066 restraints weight = 15408.494| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.91 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 11454 Z= 0.126 Angle : 0.536 6.325 15666 Z= 0.262 Chirality : 0.042 0.138 1737 Planarity : 0.005 0.057 1827 Dihedral : 13.946 123.546 1662 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 10.96 % Favored : 87.44 % 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: 1.73 (0.25), residues: 1260 helix: 1.93 (0.20), residues: 753 sheet: 0.58 (0.53), residues: 123 loop : -0.18 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.026 0.002 TYR C 427 PHE 0.014 0.001 PHE C 65 TRP 0.021 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11448) covalent geometry : angle 0.53638 / 0.26 (15666) hydrogen bonds : bond 0.04066 / 2.89 ( 582) hydrogen bonds : angle 4.69609 / 3.27 ( 1701) Misc. bond : bond 0.06376 / 3.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.252 Fit side-chains REVERT: B 65 PHE cc_start: 0.7774 (t80) cc_final: 0.7474 (t80) REVERT: B 81 ASP cc_start: 0.8834 (t0) cc_final: 0.8392 (t0) REVERT: B 456 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7927 (mtp180) REVERT: A 81 ASP cc_start: 0.8834 (t0) cc_final: 0.8363 (t0) REVERT: A 325 MET cc_start: 0.5277 (mmt) cc_final: 0.3455 (ptp) REVERT: A 417 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7058 (mtp-110) REVERT: C 80 GLU cc_start: 0.8118 (mp0) cc_final: 0.7740 (mp0) REVERT: C 81 ASP cc_start: 0.8802 (t0) cc_final: 0.8381 (t0) REVERT: C 325 MET cc_start: 0.4884 (mmt) cc_final: 0.3826 (ppp) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.0831 time to fit residues: 12.8487 Evaluate side-chains 101 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.150928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119916 restraints weight = 15502.459| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.91 r_work: 0.3365 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 11454 Z= 0.126 Angle : 0.534 6.556 15666 Z= 0.260 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.056 1827 Dihedral : 13.703 121.380 1662 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.68 % Allowed : 11.23 % Favored : 87.09 % 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: 1.74 (0.25), residues: 1260 helix: 1.92 (0.20), residues: 753 sheet: 0.78 (0.54), residues: 120 loop : -0.19 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.027 0.002 TYR C 427 PHE 0.008 0.001 PHE A 65 TRP 0.023 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11448) covalent geometry : angle 0.53394 / 0.26 (15666) hydrogen bonds : bond 0.04068 / 2.89 ( 582) hydrogen bonds : angle 4.68352 / 3.26 ( 1701) Misc. bond : bond 0.06848 / 4.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.402 Fit side-chains REVERT: B 65 PHE cc_start: 0.7936 (t80) cc_final: 0.7613 (t80) REVERT: B 81 ASP cc_start: 0.8868 (t0) cc_final: 0.8421 (t0) REVERT: B 275 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 456 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7948 (mtp180) REVERT: A 81 ASP cc_start: 0.8842 (t0) cc_final: 0.8355 (t0) REVERT: A 325 MET cc_start: 0.5675 (mmt) cc_final: 0.4037 (ptp) REVERT: A 417 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7051 (mtp-110) REVERT: C 80 GLU cc_start: 0.8095 (mp0) cc_final: 0.7715 (mp0) REVERT: C 81 ASP cc_start: 0.8853 (t0) cc_final: 0.8387 (t0) REVERT: C 325 MET cc_start: 0.5237 (mmt) cc_final: 0.4109 (ppp) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.0770 time to fit residues: 12.4378 Evaluate side-chains 106 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122154 restraints weight = 15414.572| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.88 r_work: 0.3404 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 11454 Z= 0.107 Angle : 0.511 5.600 15666 Z= 0.249 Chirality : 0.041 0.187 1737 Planarity : 0.005 0.056 1827 Dihedral : 13.387 118.029 1662 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.24 % Allowed : 12.64 % Favored : 86.12 % 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: 1.86 (0.25), residues: 1260 helix: 2.03 (0.20), residues: 753 sheet: 0.74 (0.53), residues: 120 loop : -0.15 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.026 0.001 TYR C 427 PHE 0.018 0.001 PHE A 65 TRP 0.019 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11448) covalent geometry : angle 0.51139 / 0.25 (15666) hydrogen bonds : bond 0.03855 / 2.73 ( 582) hydrogen bonds : angle 4.60210 / 3.20 ( 1701) Misc. bond : bond 0.05786 / 3.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.329 Fit side-chains REVERT: B 65 PHE cc_start: 0.7891 (t80) cc_final: 0.7597 (t80) REVERT: B 81 ASP cc_start: 0.8880 (t0) cc_final: 0.8396 (t0) REVERT: B 275 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8430 (mm) REVERT: B 456 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7980 (mtp180) REVERT: B 463 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7879 (ttpt) REVERT: A 81 ASP cc_start: 0.8852 (t0) cc_final: 0.8330 (t0) REVERT: A 325 MET cc_start: 0.5717 (mmt) cc_final: 0.4555 (ptp) REVERT: A 417 ARG cc_start: 0.7360 (mtp85) cc_final: 0.7097 (mtp-110) REVERT: C 80 GLU cc_start: 0.8068 (mp0) cc_final: 0.7669 (mp0) REVERT: C 81 ASP cc_start: 0.8897 (t0) cc_final: 0.8438 (t0) REVERT: C 325 MET cc_start: 0.4992 (mmt) cc_final: 0.3889 (ppp) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.0894 time to fit residues: 14.1668 Evaluate side-chains 105 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.152765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121966 restraints weight = 15424.555| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.87 r_work: 0.3392 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 11454 Z= 0.111 Angle : 0.516 5.769 15666 Z= 0.250 Chirality : 0.042 0.223 1737 Planarity : 0.005 0.056 1827 Dihedral : 13.264 116.977 1662 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 13.26 % Favored : 85.50 % 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: 1.89 (0.25), residues: 1260 helix: 2.03 (0.20), residues: 753 sheet: 0.84 (0.53), residues: 120 loop : -0.11 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.033 0.001 TYR B 427 PHE 0.008 0.001 PHE A 90 TRP 0.020 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (11448) covalent geometry : angle 0.51588 / 0.25 (15666) hydrogen bonds : bond 0.03845 / 2.73 ( 582) hydrogen bonds : angle 4.58062 / 3.18 ( 1701) Misc. bond : bond 0.05929 / 3.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.388 Fit side-chains REVERT: B 65 PHE cc_start: 0.7900 (t80) cc_final: 0.7611 (t80) REVERT: B 81 ASP cc_start: 0.8900 (t0) cc_final: 0.8415 (t0) REVERT: B 275 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 456 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7945 (mtp180) REVERT: A 81 ASP cc_start: 0.8870 (t0) cc_final: 0.8380 (t0) REVERT: A 325 MET cc_start: 0.5635 (mmt) cc_final: 0.4486 (ptp) REVERT: A 417 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7091 (mtp-110) REVERT: C 80 GLU cc_start: 0.8077 (mp0) cc_final: 0.7687 (mp0) REVERT: C 81 ASP cc_start: 0.8951 (t0) cc_final: 0.8474 (t0) REVERT: C 204 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8913 (tt) REVERT: C 325 MET cc_start: 0.4935 (mmt) cc_final: 0.3876 (ppp) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.0761 time to fit residues: 12.5445 Evaluate side-chains 106 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 122 optimal weight: 0.0000 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123373 restraints weight = 14630.170| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.79 r_work: 0.3436 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11454 Z= 0.100 Angle : 0.498 5.097 15666 Z= 0.243 Chirality : 0.041 0.196 1737 Planarity : 0.005 0.056 1827 Dihedral : 12.951 112.981 1662 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.06 % Allowed : 14.15 % Favored : 84.79 % 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 (0.25), residues: 1260 helix: 2.15 (0.20), residues: 753 sheet: 0.91 (0.53), residues: 120 loop : -0.06 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.032 0.001 TYR B 427 PHE 0.019 0.001 PHE C 65 TRP 0.018 0.001 TRP C 355 HIS 0.002 0.000 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (11448) covalent geometry : angle 0.49775 / 0.24 (15666) hydrogen bonds : bond 0.03653 / 2.57 ( 582) hydrogen bonds : angle 4.49514 / 3.11 ( 1701) Misc. bond : bond 0.04522 / 2.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.405 Fit side-chains REVERT: B 65 PHE cc_start: 0.7863 (t80) cc_final: 0.7595 (t80) REVERT: B 81 ASP cc_start: 0.8898 (t0) cc_final: 0.8425 (t0) REVERT: B 275 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8372 (mm) REVERT: B 456 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7932 (mtp180) REVERT: B 463 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7672 (tttm) REVERT: A 81 ASP cc_start: 0.8858 (t0) cc_final: 0.8393 (t0) REVERT: A 325 MET cc_start: 0.5575 (mmt) cc_final: 0.4376 (ptp) REVERT: A 417 ARG cc_start: 0.7258 (mtp85) cc_final: 0.7022 (mtp-110) REVERT: C 80 GLU cc_start: 0.8082 (mp0) cc_final: 0.7693 (mp0) REVERT: C 81 ASP cc_start: 0.9006 (t0) cc_final: 0.8548 (t0) REVERT: C 184 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: C 204 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8894 (tt) REVERT: C 325 MET cc_start: 0.5108 (mmt) cc_final: 0.4084 (ppp) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.0876 time to fit residues: 13.4259 Evaluate side-chains 103 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119396 restraints weight = 15611.331| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.88 r_work: 0.3361 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 11454 Z= 0.157 Angle : 0.560 7.496 15666 Z= 0.269 Chirality : 0.043 0.211 1737 Planarity : 0.005 0.080 1827 Dihedral : 13.158 114.109 1662 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.88 % Allowed : 13.97 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.80 (0.25), residues: 1260 helix: 1.92 (0.19), residues: 753 sheet: 0.87 (0.53), residues: 120 loop : -0.08 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 183 TYR 0.030 0.002 TYR B 427 PHE 0.008 0.001 PHE C 70 TRP 0.020 0.001 TRP B 355 HIS 0.005 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (11448) covalent geometry : angle 0.56044 / 0.27 (15666) hydrogen bonds : bond 0.04136 / 2.95 ( 582) hydrogen bonds : angle 4.62563 / 3.21 ( 1701) Misc. bond : bond 0.06390 / 3.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.340 Fit side-chains REVERT: B 65 PHE cc_start: 0.7887 (t80) cc_final: 0.7434 (t80) REVERT: B 81 ASP cc_start: 0.8904 (t0) cc_final: 0.8416 (t0) REVERT: B 275 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 456 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7942 (mtp180) REVERT: A 81 ASP cc_start: 0.8871 (t0) cc_final: 0.8401 (t0) REVERT: A 325 MET cc_start: 0.5624 (mmt) cc_final: 0.4383 (ptp) REVERT: A 417 ARG cc_start: 0.7317 (mtp85) cc_final: 0.7062 (mtp-110) REVERT: C 80 GLU cc_start: 0.8088 (mp0) cc_final: 0.7708 (mp0) REVERT: C 81 ASP cc_start: 0.9017 (t0) cc_final: 0.8550 (t0) REVERT: C 204 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8934 (tt) REVERT: C 325 MET cc_start: 0.5106 (mmt) cc_final: 0.4109 (ppp) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.0806 time to fit residues: 12.7870 Evaluate side-chains 105 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120998 restraints weight = 15471.232| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.89 r_work: 0.3386 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 11454 Z= 0.117 Angle : 0.522 5.961 15666 Z= 0.252 Chirality : 0.042 0.204 1737 Planarity : 0.005 0.072 1827 Dihedral : 13.008 111.188 1662 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.06 % Allowed : 14.24 % Favored : 84.70 % 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: 1.90 (0.25), residues: 1260 helix: 2.02 (0.19), residues: 753 sheet: 0.90 (0.53), residues: 120 loop : -0.07 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.030 0.001 TYR B 427 PHE 0.019 0.001 PHE C 65 TRP 0.019 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11448) covalent geometry : angle 0.52192 / 0.25 (15666) hydrogen bonds : bond 0.03940 / 2.79 ( 582) hydrogen bonds : angle 4.56722 / 3.16 ( 1701) Misc. bond : bond 0.06094 / 3.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.38 seconds wall clock time: 38 minutes 20.40 seconds (2300.40 seconds total)