Starting phenix.real_space_refine on Wed Mar 4 08:04:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tai_25775/03_2026/7tai_25775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tai_25775/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tai_25775/03_2026/7tai_25775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tai_25775/03_2026/7tai_25775.map" model { file = "/net/cci-nas-00/data/ceres_data/7tai_25775/03_2026/7tai_25775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tai_25775/03_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-5986/lib/python3.9/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: 2.86, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 476.8 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: 0.35 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: 2.01 Time building geometry restraints manager: 1.23 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 - 31.05: 6786 31.05 - 62.10: 312 62.10 - 93.15: 30 93.15 - 124.20: 27 124.20 - 155.24: 6 Dihedral angle restraints: 7161 sinusoidal: 3402 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 7158 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: 0.01 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: 0.870 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 19.148 155.244 4731 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 covalent geometry : bond 0.00648 (11448) covalent geometry : angle 0.85703 (15666) hydrogen bonds : bond 0.11828 ( 582) hydrogen bonds : angle 5.94906 ( 1701) Misc. bond : bond 0.25464 ( 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 : 0.397 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: 0.1230 time to fit residues: 18.9183 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 : 0.398 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3902 r_free = 0.3902 target = 0.149820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119073 restraints weight = 15324.960| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.92 r_work: 0.3355 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11454 Z= 0.150 Angle : 0.644 8.664 15666 Z= 0.308 Chirality : 0.045 0.222 1737 Planarity : 0.006 0.059 1827 Dihedral : 15.922 132.757 2302 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.62 % Allowed : 5.57 % Favored : 93.81 % 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: 1.25 (0.24), residues: 1260 helix: 1.61 (0.19), residues: 747 sheet: 0.29 (0.51), residues: 123 loop : -0.44 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 456 TYR 0.036 0.002 TYR C 360 PHE 0.020 0.001 PHE A 65 TRP 0.020 0.001 TRP A 355 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00344 (11448) covalent geometry : angle 0.64359 (15666) hydrogen bonds : bond 0.04686 ( 582) hydrogen bonds : angle 4.96506 ( 1701) Misc. bond : bond 0.02917 ( 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 98 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.390 Fit side-chains REVERT: B 65 PHE cc_start: 0.7678 (t80) cc_final: 0.7435 (t80) REVERT: B 81 ASP cc_start: 0.8581 (t0) cc_final: 0.8331 (t0) REVERT: A 64 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8484 (pttm) REVERT: A 325 MET cc_start: 0.5660 (mmt) cc_final: 0.3681 (ptp) REVERT: C 80 GLU cc_start: 0.8139 (mp0) cc_final: 0.7845 (mp0) REVERT: C 81 ASP cc_start: 0.8641 (t0) cc_final: 0.8416 (t0) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.0884 time to fit residues: 12.7609 Evaluate side-chains 85 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.9980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102537 restraints weight = 14657.940| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.69 r_work: 0.3021 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 11454 Z= 0.127 Angle : 0.557 5.843 15666 Z= 0.273 Chirality : 0.043 0.149 1737 Planarity : 0.005 0.058 1827 Dihedral : 14.250 127.889 2292 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 8.22 % Favored : 90.36 % 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: 1.56 (0.25), residues: 1260 helix: 1.89 (0.20), residues: 729 sheet: 0.31 (0.47), residues: 141 loop : -0.27 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.029 0.002 TYR C 360 PHE 0.013 0.001 PHE A 65 TRP 0.024 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00298 (11448) covalent geometry : angle 0.55674 (15666) hydrogen bonds : bond 0.04357 ( 582) hydrogen bonds : angle 4.80975 ( 1701) Misc. bond : bond 0.06326 ( 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 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.439 Fit side-chains REVERT: B 65 PHE cc_start: 0.7833 (t80) cc_final: 0.7575 (t80) REVERT: B 81 ASP cc_start: 0.8694 (t0) cc_final: 0.8361 (t0) REVERT: A 81 ASP cc_start: 0.8788 (t0) cc_final: 0.8571 (t0) REVERT: A 325 MET cc_start: 0.5523 (mmt) cc_final: 0.3882 (ptp) REVERT: A 417 ARG cc_start: 0.7234 (mtp85) cc_final: 0.7026 (mtp-110) REVERT: C 80 GLU cc_start: 0.7993 (mp0) cc_final: 0.7639 (mp0) REVERT: C 81 ASP cc_start: 0.8743 (t0) cc_final: 0.8337 (t0) REVERT: C 463 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7727 (ttpt) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1080 time to fit residues: 16.9295 Evaluate side-chains 96 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 77 THR 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 463 LYS 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: 2.9990 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** 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 = 0.3559 r_free = 0.3559 target = 0.131707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102420 restraints weight = 14696.275| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.67 r_work: 0.3025 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 11454 Z= 0.129 Angle : 0.550 6.595 15666 Z= 0.267 Chirality : 0.043 0.140 1737 Planarity : 0.005 0.058 1827 Dihedral : 13.733 124.960 2292 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.68 % Allowed : 10.26 % Favored : 88.06 % 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: 1.68 (0.25), residues: 1260 helix: 1.99 (0.20), residues: 729 sheet: 0.31 (0.48), residues: 141 loop : -0.18 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.026 0.002 TYR A 360 PHE 0.012 0.001 PHE A 65 TRP 0.021 0.001 TRP A 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00306 (11448) covalent geometry : angle 0.54985 (15666) hydrogen bonds : bond 0.04214 ( 582) hydrogen bonds : angle 4.71212 ( 1701) Misc. bond : bond 0.07428 ( 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 114 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.344 Fit side-chains REVERT: B 65 PHE cc_start: 0.7873 (t80) cc_final: 0.7619 (t80) REVERT: B 81 ASP cc_start: 0.8804 (t0) cc_final: 0.8400 (t0) REVERT: A 81 ASP cc_start: 0.8880 (t0) cc_final: 0.8586 (t0) REVERT: A 325 MET cc_start: 0.5491 (mmt) cc_final: 0.3268 (ptp) REVERT: A 417 ARG cc_start: 0.7341 (mtp85) cc_final: 0.7118 (mtp-110) REVERT: C 80 GLU cc_start: 0.7963 (mp0) cc_final: 0.7581 (mp0) REVERT: C 81 ASP cc_start: 0.8860 (t0) cc_final: 0.8430 (t0) REVERT: C 325 MET cc_start: 0.5901 (mmt) cc_final: 0.4588 (ptm) REVERT: C 463 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.8013 (ttpt) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.1011 time to fit residues: 16.5128 Evaluate side-chains 101 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR 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 Chi-restraints excluded: chain C residue 463 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** 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 = 0.3559 r_free = 0.3559 target = 0.131607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104328 restraints weight = 14501.070| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.48 r_work: 0.3057 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 11454 Z= 0.120 Angle : 0.537 6.013 15666 Z= 0.260 Chirality : 0.042 0.135 1737 Planarity : 0.005 0.057 1827 Dihedral : 13.318 122.861 2292 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.21 % Allowed : 10.88 % Favored : 86.91 % 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: 1.92 (0.20), residues: 753 sheet: 0.72 (0.53), residues: 120 loop : -0.18 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 417 TYR 0.026 0.002 TYR C 427 PHE 0.010 0.001 PHE A 65 TRP 0.021 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00279 (11448) covalent geometry : angle 0.53653 (15666) hydrogen bonds : bond 0.04080 ( 582) hydrogen bonds : angle 4.65193 ( 1701) Misc. bond : bond 0.07089 ( 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 121 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.368 Fit side-chains REVERT: B 65 PHE cc_start: 0.7905 (t80) cc_final: 0.7692 (t80) REVERT: B 81 ASP cc_start: 0.8772 (t0) cc_final: 0.8390 (t0) REVERT: B 275 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 81 ASP cc_start: 0.8895 (t0) cc_final: 0.8578 (t0) REVERT: A 325 MET cc_start: 0.5198 (mmt) cc_final: 0.3624 (ptp) REVERT: C 80 GLU cc_start: 0.7872 (mp0) cc_final: 0.7556 (mp0) REVERT: C 81 ASP cc_start: 0.8864 (t0) cc_final: 0.8463 (t0) REVERT: C 325 MET cc_start: 0.5194 (mmt) cc_final: 0.4259 (ppp) outliers start: 25 outliers final: 14 residues processed: 117 average time/residue: 0.1007 time to fit residues: 17.6727 Evaluate side-chains 106 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 77 THR 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 195 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 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.131179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103846 restraints weight = 14567.669| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.49 r_work: 0.3048 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 11454 Z= 0.127 Angle : 0.535 6.392 15666 Z= 0.258 Chirality : 0.042 0.137 1737 Planarity : 0.005 0.057 1827 Dihedral : 13.103 121.194 2292 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.59 % Allowed : 11.85 % Favored : 86.56 % 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: 1.93 (0.20), residues: 753 sheet: 0.76 (0.54), residues: 120 loop : -0.20 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 417 TYR 0.025 0.002 TYR C 427 PHE 0.016 0.001 PHE A 65 TRP 0.020 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00301 (11448) covalent geometry : angle 0.53519 (15666) hydrogen bonds : bond 0.04105 ( 582) hydrogen bonds : angle 4.64876 ( 1701) Misc. bond : bond 0.07346 ( 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 114 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.421 Fit side-chains REVERT: B 65 PHE cc_start: 0.7971 (t80) cc_final: 0.7751 (t80) REVERT: B 81 ASP cc_start: 0.8814 (t0) cc_final: 0.8427 (t0) REVERT: B 275 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 81 ASP cc_start: 0.8903 (t0) cc_final: 0.8554 (t0) REVERT: A 325 MET cc_start: 0.5963 (mmt) cc_final: 0.4649 (ptp) REVERT: C 80 GLU cc_start: 0.7839 (mp0) cc_final: 0.7517 (mp0) REVERT: C 81 ASP cc_start: 0.8886 (t0) cc_final: 0.8475 (t0) REVERT: C 325 MET cc_start: 0.5192 (mmt) cc_final: 0.4190 (ppp) outliers start: 18 outliers final: 15 residues processed: 108 average time/residue: 0.0973 time to fit residues: 15.9622 Evaluate side-chains 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 77 THR 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 195 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 444 LEU Chi-restraints excluded: chain C residue 466 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.131503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102972 restraints weight = 14435.113| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.59 r_work: 0.3042 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 11454 Z= 0.121 Angle : 0.525 6.210 15666 Z= 0.254 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.057 1827 Dihedral : 12.760 117.968 2292 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.68 % Allowed : 12.11 % Favored : 86.21 % 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: 1.96 (0.20), residues: 753 sheet: 0.81 (0.54), residues: 120 loop : -0.16 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 417 TYR 0.026 0.001 TYR C 427 PHE 0.009 0.001 PHE A 65 TRP 0.020 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00286 (11448) covalent geometry : angle 0.52544 (15666) hydrogen bonds : bond 0.04033 ( 582) hydrogen bonds : angle 4.61810 ( 1701) Misc. bond : bond 0.07110 ( 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.456 Fit side-chains REVERT: B 65 PHE cc_start: 0.7990 (t80) cc_final: 0.7769 (t80) REVERT: B 81 ASP cc_start: 0.8851 (t0) cc_final: 0.8408 (t0) REVERT: B 275 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 81 ASP cc_start: 0.8946 (t0) cc_final: 0.8549 (t0) REVERT: A 325 MET cc_start: 0.5737 (mmt) cc_final: 0.4540 (ptp) REVERT: C 80 GLU cc_start: 0.7907 (mp0) cc_final: 0.7559 (mp0) REVERT: C 81 ASP cc_start: 0.8944 (t0) cc_final: 0.8494 (t0) REVERT: C 204 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8903 (tt) REVERT: C 325 MET cc_start: 0.5230 (mmt) cc_final: 0.4229 (ppp) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 0.0930 time to fit residues: 16.2500 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 77 THR 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 195 LEU 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 Chi-restraints excluded: chain C residue 466 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3567 r_free = 0.3567 target = 0.132014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103617 restraints weight = 14441.323| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.58 r_work: 0.3050 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 11454 Z= 0.113 Angle : 0.514 5.848 15666 Z= 0.249 Chirality : 0.042 0.135 1737 Planarity : 0.005 0.056 1827 Dihedral : 12.544 116.006 2292 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.68 % Allowed : 12.56 % Favored : 85.76 % 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: 2.01 (0.20), residues: 753 sheet: 0.78 (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 0.031 0.001 TYR B 427 PHE 0.020 0.001 PHE A 65 TRP 0.019 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00262 (11448) covalent geometry : angle 0.51421 (15666) hydrogen bonds : bond 0.03925 ( 582) hydrogen bonds : angle 4.57236 ( 1701) Misc. bond : bond 0.06656 ( 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.361 Fit side-chains REVERT: B 65 PHE cc_start: 0.7969 (t80) cc_final: 0.7761 (t80) REVERT: B 81 ASP cc_start: 0.8862 (t0) cc_final: 0.8419 (t0) REVERT: B 275 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 81 ASP cc_start: 0.8887 (t0) cc_final: 0.8489 (t0) REVERT: A 325 MET cc_start: 0.5710 (mmt) cc_final: 0.4580 (ptp) REVERT: C 80 GLU cc_start: 0.7890 (mp0) cc_final: 0.7552 (mp0) REVERT: C 81 ASP cc_start: 0.8950 (t0) cc_final: 0.8496 (t0) REVERT: C 204 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 325 MET cc_start: 0.5106 (mmt) cc_final: 0.4111 (ppp) outliers start: 19 outliers final: 17 residues processed: 116 average time/residue: 0.0948 time to fit residues: 16.5689 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 B residue 354 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR 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 195 LEU 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 Chi-restraints excluded: chain C residue 466 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 0.0020 chunk 88 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN B 171 ASN B 173 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103850 restraints weight = 14351.167| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.45 r_work: 0.3037 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 11454 Z= 0.130 Angle : 0.534 6.565 15666 Z= 0.258 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.056 1827 Dihedral : 12.478 115.089 2292 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.03 % Allowed : 12.82 % 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: 1.96 (0.20), residues: 753 sheet: 0.74 (0.52), residues: 120 loop : -0.11 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.032 0.002 TYR B 427 PHE 0.018 0.001 PHE C 65 TRP 0.018 0.001 TRP C 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00312 (11448) covalent geometry : angle 0.53408 (15666) hydrogen bonds : bond 0.04069 ( 582) hydrogen bonds : angle 4.61229 ( 1701) Misc. bond : bond 0.07169 ( 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.421 Fit side-chains REVERT: B 81 ASP cc_start: 0.8795 (t0) cc_final: 0.8399 (t0) REVERT: B 275 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 81 ASP cc_start: 0.8871 (t0) cc_final: 0.8507 (t0) REVERT: A 325 MET cc_start: 0.5702 (mmt) cc_final: 0.4613 (ptp) REVERT: C 80 GLU cc_start: 0.7779 (mp0) cc_final: 0.7469 (mp0) REVERT: C 81 ASP cc_start: 0.8931 (t0) cc_final: 0.8495 (t0) REVERT: C 204 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8892 (tt) REVERT: C 325 MET cc_start: 0.5174 (mmt) cc_final: 0.4282 (ppp) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.0903 time to fit residues: 15.4976 Evaluate side-chains 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU 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 Chi-restraints excluded: chain C residue 466 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3585 r_free = 0.3585 target = 0.133416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104188 restraints weight = 14625.413| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.69 r_work: 0.3064 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1985 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= 0.108 Angle : 0.508 5.113 15666 Z= 0.247 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.056 1827 Dihedral : 12.169 111.643 2292 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.24 % Allowed : 13.44 % Favored : 85.32 % 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: 1.94 (0.25), residues: 1260 helix: 2.07 (0.20), residues: 753 sheet: 0.82 (0.52), 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 0.031 0.001 TYR B 427 PHE 0.020 0.001 PHE A 65 TRP 0.019 0.001 TRP B 355 HIS 0.002 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00251 (11448) covalent geometry : angle 0.50767 (15666) hydrogen bonds : bond 0.03832 ( 582) hydrogen bonds : angle 4.54017 ( 1701) Misc. bond : bond 0.06062 ( 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 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.416 Fit side-chains REVERT: B 81 ASP cc_start: 0.8885 (t0) cc_final: 0.8385 (t0) REVERT: B 275 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8441 (mm) REVERT: A 81 ASP cc_start: 0.8930 (t0) cc_final: 0.8496 (t0) REVERT: A 325 MET cc_start: 0.5589 (mmt) cc_final: 0.4427 (ptp) REVERT: C 80 GLU cc_start: 0.7988 (mp0) cc_final: 0.7626 (mp0) REVERT: C 81 ASP cc_start: 0.8975 (t0) cc_final: 0.8479 (t0) REVERT: C 204 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8808 (tt) REVERT: C 325 MET cc_start: 0.5212 (mmt) cc_final: 0.4223 (ppp) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.0931 time to fit residues: 15.6878 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 : 0.445 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain C residue 195 LEU 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 Chi-restraints excluded: chain C residue 466 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.131556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102664 restraints weight = 14560.243| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.62 r_work: 0.3028 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11454 Z= 0.134 Angle : 0.535 6.582 15666 Z= 0.258 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.080 1827 Dihedral : 12.193 111.194 2292 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 13.26 % Favored : 85.32 % 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: 1.81 (0.25), residues: 1260 helix: 1.95 (0.19), residues: 753 sheet: 0.84 (0.53), residues: 120 loop : -0.10 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.031 0.002 TYR B 427 PHE 0.027 0.001 PHE B 65 TRP 0.019 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00326 (11448) covalent geometry : angle 0.53510 (15666) hydrogen bonds : bond 0.04056 ( 582) hydrogen bonds : angle 4.59484 ( 1701) Misc. bond : bond 0.06915 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.99 seconds wall clock time: 45 minutes 51.77 seconds (2751.77 seconds total)