Starting phenix.real_space_refine on Mon Dec 30 03:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tai_25775/12_2024/7tai_25775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tai_25775/12_2024/7tai_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_25775/12_2024/7tai_25775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tai_25775/12_2024/7tai_25775.map" model { file = "/net/cci-nas-00/data/ceres_data/7tai_25775/12_2024/7tai_25775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tai_25775/12_2024/7tai_25775.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11109 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B Time building chain proxies: 7.78, per 1000 atoms: 0.70 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: 3.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.84 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: 3.13 Time building geometry restraints manager: 3.65 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.830 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.640 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- 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 : 0.006 0.142 11448 Z= 0.403 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.011 0.001 TRP C 355 HIS 0.005 0.001 HIS B 79 PHE 0.021 0.002 PHE A 69 TYR 0.023 0.002 TYR B 271 ARG 0.009 0.001 ARG C 456 *********************** 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 : 1.238 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: 0.2675 time to fit residues: 42.0819 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 : 1.466 ------------------------------------------------------------------------------- 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 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11448 Z= 0.217 Angle : 0.641 8.738 15666 Z= 0.306 Chirality : 0.044 0.217 1737 Planarity : 0.006 0.059 1827 Dihedral : 15.846 132.308 2302 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.62 % Allowed : 5.92 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1260 helix: 1.59 (0.19), residues: 747 sheet: 0.30 (0.51), residues: 123 loop : -0.45 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 355 HIS 0.004 0.001 HIS A 409 PHE 0.019 0.001 PHE A 65 TYR 0.038 0.002 TYR C 360 ARG 0.005 0.000 ARG C 456 *********************** 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 : 1.212 Fit side-chains REVERT: B 60 SER cc_start: 0.8725 (t) cc_final: 0.8456 (p) REVERT: B 65 PHE cc_start: 0.7505 (t80) cc_final: 0.7267 (t80) REVERT: B 81 ASP cc_start: 0.8480 (t0) cc_final: 0.8210 (t0) REVERT: C 80 GLU cc_start: 0.7884 (mp0) cc_final: 0.7611 (mp0) REVERT: C 81 ASP cc_start: 0.8593 (t0) cc_final: 0.8352 (t0) REVERT: C 358 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7604 (mt-10) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2063 time to fit residues: 29.8601 Evaluate side-chains 89 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11448 Z= 0.223 Angle : 0.577 6.531 15666 Z= 0.281 Chirality : 0.044 0.154 1737 Planarity : 0.005 0.058 1827 Dihedral : 14.474 128.254 2292 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.50 % Allowed : 8.05 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1260 helix: 1.81 (0.20), residues: 729 sheet: 0.56 (0.52), residues: 120 loop : -0.30 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 PHE 0.008 0.001 PHE A 65 TYR 0.029 0.002 TYR C 360 ARG 0.003 0.000 ARG B 175 *********************** 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 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.292 Fit side-chains REVERT: B 65 PHE cc_start: 0.7599 (t80) cc_final: 0.7362 (t80) REVERT: B 81 ASP cc_start: 0.8575 (t0) cc_final: 0.8243 (t0) REVERT: A 325 MET cc_start: 0.5313 (mmt) cc_final: 0.3188 (ptp) REVERT: C 80 GLU cc_start: 0.7915 (mp0) cc_final: 0.7599 (mp0) REVERT: C 81 ASP cc_start: 0.8662 (t0) cc_final: 0.8313 (t0) REVERT: C 325 MET cc_start: 0.5687 (mmt) cc_final: 0.4523 (ptm) REVERT: C 358 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7627 (mt-10) outliers start: 17 outliers final: 12 residues processed: 106 average time/residue: 0.2318 time to fit residues: 35.9193 Evaluate side-chains 99 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.0770 chunk 32 optimal weight: 0.3980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11448 Z= 0.151 Angle : 0.522 6.293 15666 Z= 0.257 Chirality : 0.042 0.139 1737 Planarity : 0.005 0.057 1827 Dihedral : 13.620 123.827 2292 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.15 % Allowed : 10.61 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1260 helix: 2.11 (0.20), residues: 729 sheet: 0.47 (0.48), residues: 138 loop : -0.22 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 355 HIS 0.002 0.000 HIS C 409 PHE 0.019 0.001 PHE A 65 TYR 0.026 0.001 TYR C 360 ARG 0.007 0.000 ARG A 417 *********************** 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7562 (t80) cc_final: 0.7309 (t80) REVERT: B 81 ASP cc_start: 0.8619 (t0) cc_final: 0.8227 (t0) REVERT: A 81 ASP cc_start: 0.8664 (t0) cc_final: 0.8388 (t0) REVERT: A 325 MET cc_start: 0.5427 (mmt) cc_final: 0.3894 (ptp) REVERT: C 80 GLU cc_start: 0.7822 (mp0) cc_final: 0.7486 (mp0) REVERT: C 81 ASP cc_start: 0.8717 (t0) cc_final: 0.8306 (t0) REVERT: C 358 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7631 (mt-10) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.2274 time to fit residues: 39.0038 Evaluate side-chains 96 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 77 THR 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 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 101 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11448 Z= 0.301 Angle : 0.622 8.849 15666 Z= 0.297 Chirality : 0.045 0.141 1737 Planarity : 0.005 0.058 1827 Dihedral : 13.641 125.634 2292 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.03 % Allowed : 11.32 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1260 helix: 1.78 (0.20), residues: 735 sheet: 0.53 (0.52), residues: 120 loop : -0.14 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 355 HIS 0.005 0.001 HIS C 409 PHE 0.011 0.001 PHE A 65 TYR 0.028 0.002 TYR C 427 ARG 0.003 0.000 ARG C 417 *********************** 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 119 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8717 (t0) cc_final: 0.8280 (t0) REVERT: B 275 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 81 ASP cc_start: 0.8791 (t0) cc_final: 0.8451 (t0) REVERT: A 325 MET cc_start: 0.5326 (mmt) cc_final: 0.3805 (ptp) REVERT: C 80 GLU cc_start: 0.7945 (mp0) cc_final: 0.7576 (mp0) REVERT: C 81 ASP cc_start: 0.8789 (t0) cc_final: 0.8315 (t0) REVERT: C 358 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7607 (mt-10) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 0.2273 time to fit residues: 38.3283 Evaluate side-chains 107 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain B residue 463 LYS 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 40 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11448 Z= 0.247 Angle : 0.576 7.563 15666 Z= 0.277 Chirality : 0.044 0.139 1737 Planarity : 0.005 0.058 1827 Dihedral : 13.354 121.677 2292 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.03 % Allowed : 11.94 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1260 helix: 1.81 (0.20), residues: 735 sheet: 0.55 (0.49), residues: 138 loop : -0.14 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 PHE 0.015 0.001 PHE B 65 TYR 0.027 0.002 TYR C 427 ARG 0.004 0.000 ARG A 105 *********************** 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 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.269 Fit side-chains REVERT: B 81 ASP cc_start: 0.8741 (t0) cc_final: 0.8289 (t0) REVERT: B 275 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8498 (mm) REVERT: B 415 TRP cc_start: 0.6654 (t60) cc_final: 0.6430 (t60) REVERT: A 81 ASP cc_start: 0.8808 (t0) cc_final: 0.8434 (t0) REVERT: A 325 MET cc_start: 0.5553 (mmt) cc_final: 0.4167 (ptp) REVERT: C 80 GLU cc_start: 0.7941 (mp0) cc_final: 0.7578 (mp0) REVERT: C 81 ASP cc_start: 0.8809 (t0) cc_final: 0.8356 (t0) REVERT: C 204 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8760 (tt) REVERT: C 325 MET cc_start: 0.5138 (mmt) cc_final: 0.4112 (ppp) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.2172 time to fit residues: 37.3715 Evaluate side-chains 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain B residue 466 GLU 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 466 GLU 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 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 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11448 Z= 0.190 Angle : 0.545 7.174 15666 Z= 0.265 Chirality : 0.043 0.196 1737 Planarity : 0.005 0.058 1827 Dihedral : 13.061 119.994 2292 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1260 helix: 1.92 (0.20), residues: 735 sheet: 0.67 (0.49), residues: 138 loop : -0.10 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 PHE 0.016 0.001 PHE A 65 TYR 0.027 0.001 TYR C 427 ARG 0.002 0.000 ARG C 417 *********************** 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.171 Fit side-chains REVERT: B 81 ASP cc_start: 0.8747 (t0) cc_final: 0.8297 (t0) REVERT: B 275 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8494 (mm) REVERT: A 81 ASP cc_start: 0.8805 (t0) cc_final: 0.8430 (t0) REVERT: A 325 MET cc_start: 0.5755 (mmt) cc_final: 0.4476 (ptp) REVERT: C 80 GLU cc_start: 0.7822 (mp0) cc_final: 0.7491 (mp0) REVERT: C 81 ASP cc_start: 0.8820 (t0) cc_final: 0.8353 (t0) REVERT: C 204 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8746 (tt) REVERT: C 325 MET cc_start: 0.5160 (mmt) cc_final: 0.4168 (ppp) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.1990 time to fit residues: 34.8891 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 : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR 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 A residue 466 GLU 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 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 72 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11448 Z= 0.214 Angle : 0.551 6.858 15666 Z= 0.266 Chirality : 0.043 0.197 1737 Planarity : 0.005 0.057 1827 Dihedral : 12.831 118.250 2292 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.86 % Allowed : 12.47 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1260 helix: 1.90 (0.20), residues: 735 sheet: 0.69 (0.49), residues: 138 loop : -0.05 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 355 HIS 0.004 0.001 HIS C 409 PHE 0.020 0.001 PHE B 65 TYR 0.035 0.002 TYR B 427 ARG 0.002 0.000 ARG C 417 *********************** 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 121 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.307 Fit side-chains REVERT: B 81 ASP cc_start: 0.8777 (t0) cc_final: 0.8317 (t0) REVERT: B 275 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 81 ASP cc_start: 0.8747 (t0) cc_final: 0.8333 (t0) REVERT: A 325 MET cc_start: 0.5763 (mmt) cc_final: 0.4548 (ptp) REVERT: C 80 GLU cc_start: 0.7898 (mp0) cc_final: 0.7535 (mp0) REVERT: C 81 ASP cc_start: 0.8819 (t0) cc_final: 0.8336 (t0) REVERT: C 204 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8754 (tt) REVERT: C 325 MET cc_start: 0.5336 (mmt) cc_final: 0.4310 (ppp) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.2012 time to fit residues: 36.0439 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 : 1.231 ------------------------------------------------------------------------------- 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 466 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR 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 A residue 466 GLU 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 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 113 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11448 Z= 0.212 Angle : 0.546 6.551 15666 Z= 0.264 Chirality : 0.043 0.190 1737 Planarity : 0.005 0.057 1827 Dihedral : 12.692 116.239 2292 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.86 % Allowed : 12.91 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1260 helix: 1.92 (0.20), residues: 735 sheet: 0.73 (0.49), residues: 138 loop : -0.02 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 355 HIS 0.004 0.001 HIS C 409 PHE 0.020 0.001 PHE A 65 TYR 0.032 0.002 TYR B 427 ARG 0.002 0.000 ARG A 326 *********************** 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.211 Fit side-chains REVERT: B 81 ASP cc_start: 0.8783 (t0) cc_final: 0.8330 (t0) REVERT: B 275 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 81 ASP cc_start: 0.8756 (t0) cc_final: 0.8321 (t0) REVERT: A 325 MET cc_start: 0.5637 (mmt) cc_final: 0.4651 (ptp) REVERT: C 80 GLU cc_start: 0.7936 (mp0) cc_final: 0.7577 (mp0) REVERT: C 81 ASP cc_start: 0.8837 (t0) cc_final: 0.8344 (t0) REVERT: C 204 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8757 (tt) REVERT: C 325 MET cc_start: 0.5211 (mmt) cc_final: 0.4265 (ppp) outliers start: 21 outliers final: 19 residues processed: 114 average time/residue: 0.2083 time to fit residues: 36.4813 Evaluate side-chains 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR 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 A residue 466 GLU 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 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 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11448 Z= 0.187 Angle : 0.527 5.809 15666 Z= 0.256 Chirality : 0.042 0.185 1737 Planarity : 0.005 0.057 1827 Dihedral : 12.398 113.855 2292 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.86 % Allowed : 13.17 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1260 helix: 2.00 (0.20), residues: 735 sheet: 0.78 (0.49), residues: 138 loop : 0.04 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 PHE 0.025 0.001 PHE B 65 TYR 0.032 0.001 TYR B 427 ARG 0.003 0.000 ARG A 326 ********************** 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.184 Fit side-chains REVERT: B 81 ASP cc_start: 0.8761 (t0) cc_final: 0.8312 (t0) REVERT: B 275 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 81 ASP cc_start: 0.8757 (t0) cc_final: 0.8338 (t0) REVERT: A 325 MET cc_start: 0.5629 (mmt) cc_final: 0.4659 (ptp) REVERT: C 65 PHE cc_start: 0.7679 (t80) cc_final: 0.7441 (t80) REVERT: C 80 GLU cc_start: 0.7820 (mp0) cc_final: 0.7472 (mp0) REVERT: C 81 ASP cc_start: 0.8832 (t0) cc_final: 0.8347 (t0) REVERT: C 204 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8734 (tt) REVERT: C 325 MET cc_start: 0.5090 (mmt) cc_final: 0.4172 (ppp) outliers start: 21 outliers final: 19 residues processed: 117 average time/residue: 0.1938 time to fit residues: 34.8202 Evaluate side-chains 119 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain A residue 77 THR 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 A residue 381 SER Chi-restraints excluded: chain A residue 466 GLU 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 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 30 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 0.0000 overall best weight: 0.3280 ------------------------------------------------------------------------------- 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** B 184 GLN ** A 129 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 = 0.3589 r_free = 0.3589 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107148 restraints weight = 14291.971| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.44 r_work: 0.3084 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11448 Z= 0.152 Angle : 0.508 5.117 15666 Z= 0.248 Chirality : 0.042 0.174 1737 Planarity : 0.005 0.057 1827 Dihedral : 11.950 109.665 2292 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 13.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1260 helix: 2.08 (0.20), residues: 753 sheet: 0.92 (0.53), residues: 120 loop : -0.01 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 355 HIS 0.003 0.001 HIS A 97 PHE 0.031 0.001 PHE A 65 TYR 0.031 0.001 TYR B 427 ARG 0.003 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.75 seconds wall clock time: 37 minutes 56.19 seconds (2276.19 seconds total)