Starting phenix.real_space_refine on Tue Jun 10 21:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tai_25775/06_2025/7tai_25775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tai_25775/06_2025/7tai_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_25775/06_2025/7tai_25775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tai_25775/06_2025/7tai_25775.map" model { file = "/net/cci-nas-00/data/ceres_data/7tai_25775/06_2025/7tai_25775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tai_25775/06_2025/7tai_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-5710/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: 8.01, per 1000 atoms: 0.72 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: 3.00 Conformation dependent library (CDL) restraints added in 1.3 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: 1.10 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: 3.27 Time building geometry restraints manager: 3.45 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.050 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.11828 ( 582) hydrogen bonds : angle 5.94906 ( 1701) covalent geometry : bond 0.00648 (11448) covalent geometry : angle 0.85703 (15666) 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 : 1.133 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: 0.2595 time to fit residues: 40.1444 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 : 1.186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119285 restraints weight = 15288.154| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.92 r_work: 0.3363 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 11454 Z= 0.143 Angle : 0.641 8.737 15666 Z= 0.306 Chirality : 0.044 0.217 1737 Planarity : 0.006 0.059 1827 Dihedral : 15.846 132.305 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 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 582) hydrogen bonds : angle 4.96478 ( 1701) covalent geometry : bond 0.00333 (11448) covalent geometry : angle 0.64109 (15666) Misc. bond : bond 0.02034 ( 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 : 1.265 Fit side-chains REVERT: B 65 PHE cc_start: 0.7698 (t80) cc_final: 0.7414 (t80) REVERT: B 81 ASP cc_start: 0.8590 (t0) cc_final: 0.8332 (t0) REVERT: A 64 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8490 (pttm) REVERT: C 80 GLU cc_start: 0.8136 (mp0) cc_final: 0.7840 (mp0) REVERT: C 81 ASP cc_start: 0.8646 (t0) cc_final: 0.8403 (t0) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2047 time to fit residues: 29.8816 Evaluate side-chains 87 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 84 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097912 restraints weight = 14739.882| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.68 r_work: 0.2954 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 11454 Z= 0.215 Angle : 0.658 9.391 15666 Z= 0.313 Chirality : 0.046 0.155 1737 Planarity : 0.005 0.060 1827 Dihedral : 14.604 129.361 2292 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.41 % Allowed : 9.11 % Favored : 89.48 % 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: 1.58 (0.19), residues: 729 sheet: 0.41 (0.52), residues: 120 loop : -0.36 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 355 HIS 0.006 0.001 HIS A 79 PHE 0.011 0.001 PHE A 65 TYR 0.031 0.002 TYR C 360 ARG 0.003 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 582) hydrogen bonds : angle 4.99155 ( 1701) covalent geometry : bond 0.00530 (11448) covalent geometry : angle 0.65846 (15666) Misc. bond : bond 0.11419 ( 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 113 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.326 Fit side-chains REVERT: B 65 PHE cc_start: 0.7922 (t80) cc_final: 0.7687 (t80) REVERT: B 81 ASP cc_start: 0.8754 (t0) cc_final: 0.8364 (t0) REVERT: B 415 TRP cc_start: 0.7108 (t60) cc_final: 0.6868 (t60) REVERT: B 456 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7976 (mtp180) REVERT: A 81 ASP cc_start: 0.8913 (t0) cc_final: 0.8657 (t0) REVERT: A 195 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 325 MET cc_start: 0.5501 (mmt) cc_final: 0.4131 (ptp) REVERT: A 415 TRP cc_start: 0.6941 (t60) cc_final: 0.6468 (t60) REVERT: C 80 GLU cc_start: 0.8050 (mp0) cc_final: 0.7696 (mp0) REVERT: C 81 ASP cc_start: 0.8824 (t0) cc_final: 0.8412 (t0) REVERT: C 325 MET cc_start: 0.5721 (mmt) cc_final: 0.4381 (ppp) REVERT: C 415 TRP cc_start: 0.7056 (t60) cc_final: 0.6597 (t60) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.2468 time to fit residues: 39.4569 Evaluate side-chains 103 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 195 LEU 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 86 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101398 restraints weight = 14524.326| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.69 r_work: 0.2997 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 11454 Z= 0.130 Angle : 0.558 7.256 15666 Z= 0.272 Chirality : 0.043 0.137 1737 Planarity : 0.005 0.060 1827 Dihedral : 13.860 124.104 2292 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 11.32 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.25), residues: 1260 helix: 1.88 (0.20), residues: 729 sheet: 0.40 (0.48), residues: 138 loop : -0.27 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 355 HIS 0.003 0.001 HIS C 409 PHE 0.009 0.001 PHE A 90 TYR 0.026 0.002 TYR C 360 ARG 0.004 0.000 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 582) hydrogen bonds : angle 4.81105 ( 1701) covalent geometry : bond 0.00306 (11448) covalent geometry : angle 0.55794 (15666) Misc. bond : bond 0.09592 ( 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7922 (t80) cc_final: 0.7678 (t80) REVERT: B 81 ASP cc_start: 0.8825 (t0) cc_final: 0.8411 (t0) REVERT: B 415 TRP cc_start: 0.7102 (t60) cc_final: 0.6846 (t60) REVERT: B 456 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7972 (mtp180) REVERT: A 81 ASP cc_start: 0.8875 (t0) cc_final: 0.8571 (t0) REVERT: A 325 MET cc_start: 0.5447 (mmt) cc_final: 0.3776 (ptp) REVERT: C 80 GLU cc_start: 0.8108 (mp0) cc_final: 0.7712 (mp0) REVERT: C 81 ASP cc_start: 0.8884 (t0) cc_final: 0.8432 (t0) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 0.2264 time to fit residues: 38.4551 Evaluate side-chains 104 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 381 SER 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 275 LEU 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 70 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101110 restraints weight = 14471.156| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.69 r_work: 0.2993 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 11454 Z= 0.141 Angle : 0.565 6.762 15666 Z= 0.273 Chirality : 0.043 0.137 1737 Planarity : 0.005 0.059 1827 Dihedral : 13.555 124.140 2292 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.21 % Allowed : 11.94 % Favored : 85.85 % 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: 1.90 (0.20), residues: 729 sheet: 0.43 (0.48), residues: 138 loop : -0.25 (0.32), residues: 393 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 0.014 0.001 PHE A 65 TYR 0.026 0.002 TYR C 427 ARG 0.003 0.000 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 582) hydrogen bonds : angle 4.77119 ( 1701) covalent geometry : bond 0.00337 (11448) covalent geometry : angle 0.56468 (15666) Misc. bond : bond 0.09347 ( 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 124 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7879 (t80) cc_final: 0.7647 (t80) REVERT: B 81 ASP cc_start: 0.8856 (t0) cc_final: 0.8410 (t0) REVERT: B 275 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 415 TRP cc_start: 0.7103 (t60) cc_final: 0.6841 (t60) REVERT: B 456 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7981 (mtp180) REVERT: A 81 ASP cc_start: 0.8909 (t0) cc_final: 0.8546 (t0) REVERT: A 325 MET cc_start: 0.5503 (mmt) cc_final: 0.3811 (ptp) REVERT: C 80 GLU cc_start: 0.8089 (mp0) cc_final: 0.7685 (mp0) REVERT: C 81 ASP cc_start: 0.8885 (t0) cc_final: 0.8427 (t0) REVERT: C 204 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8835 (tt) outliers start: 25 outliers final: 15 residues processed: 118 average time/residue: 0.2173 time to fit residues: 38.0465 Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103491 restraints weight = 14532.168| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.48 r_work: 0.3038 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 11454 Z= 0.124 Angle : 0.538 6.087 15666 Z= 0.260 Chirality : 0.043 0.136 1737 Planarity : 0.005 0.058 1827 Dihedral : 13.180 121.147 2292 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 11.94 % 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 (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: 1.95 (0.20), residues: 735 sheet: 0.57 (0.49), residues: 138 loop : -0.12 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.016 0.001 PHE C 65 TYR 0.028 0.002 TYR C 427 ARG 0.002 0.000 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 582) hydrogen bonds : angle 4.69293 ( 1701) covalent geometry : bond 0.00293 (11448) covalent geometry : angle 0.53804 (15666) Misc. bond : bond 0.08428 ( 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 127 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8834 (t0) cc_final: 0.8447 (t0) REVERT: B 275 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8547 (mm) REVERT: B 415 TRP cc_start: 0.6901 (t60) cc_final: 0.6699 (t60) REVERT: A 81 ASP cc_start: 0.8914 (t0) cc_final: 0.8560 (t0) REVERT: A 325 MET cc_start: 0.5706 (mmt) cc_final: 0.4256 (ptp) REVERT: C 80 GLU cc_start: 0.7808 (mp0) cc_final: 0.7468 (mp0) REVERT: C 81 ASP cc_start: 0.8894 (t0) cc_final: 0.8483 (t0) REVERT: C 204 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8858 (tt) REVERT: C 325 MET cc_start: 0.5243 (mmt) cc_final: 0.4215 (ppp) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.2089 time to fit residues: 37.4355 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 463 LYS 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 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 160 ASP 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 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 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 = 0.131704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103095 restraints weight = 14697.253| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.60 r_work: 0.3046 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 11454 Z= 0.114 Angle : 0.523 5.454 15666 Z= 0.255 Chirality : 0.042 0.135 1737 Planarity : 0.005 0.058 1827 Dihedral : 12.829 118.986 2292 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.21 % Allowed : 12.20 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.25), residues: 1260 helix: 2.05 (0.20), residues: 735 sheet: 0.73 (0.50), residues: 138 loop : -0.10 (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 B 409 PHE 0.017 0.001 PHE A 65 TYR 0.028 0.001 TYR C 427 ARG 0.002 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 582) hydrogen bonds : angle 4.62365 ( 1701) covalent geometry : bond 0.00260 (11448) covalent geometry : angle 0.52283 (15666) Misc. bond : bond 0.07447 ( 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 125 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.178 Fit side-chains REVERT: B 81 ASP cc_start: 0.8846 (t0) cc_final: 0.8446 (t0) REVERT: B 275 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 81 ASP cc_start: 0.8895 (t0) cc_final: 0.8506 (t0) REVERT: A 325 MET cc_start: 0.5897 (mmt) cc_final: 0.4505 (ptp) REVERT: C 80 GLU cc_start: 0.7877 (mp0) cc_final: 0.7526 (mp0) REVERT: C 81 ASP cc_start: 0.8932 (t0) cc_final: 0.8483 (t0) REVERT: C 204 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8880 (tt) REVERT: C 325 MET cc_start: 0.5260 (mmt) cc_final: 0.4211 (ppp) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.2066 time to fit residues: 36.5035 Evaluate side-chains 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103321 restraints weight = 14528.316| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.62 r_work: 0.3033 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 11454 Z= 0.120 Angle : 0.527 5.962 15666 Z= 0.256 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.058 1827 Dihedral : 12.679 117.642 2292 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.77 % Allowed : 13.09 % 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 (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: 2.04 (0.20), residues: 735 sheet: 0.77 (0.49), residues: 138 loop : -0.07 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.019 0.001 PHE C 65 TYR 0.034 0.002 TYR B 427 ARG 0.002 0.000 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 582) hydrogen bonds : angle 4.61217 ( 1701) covalent geometry : bond 0.00284 (11448) covalent geometry : angle 0.52729 (15666) Misc. bond : bond 0.07377 ( 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 123 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.278 Fit side-chains REVERT: B 81 ASP cc_start: 0.8834 (t0) cc_final: 0.8386 (t0) REVERT: B 275 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8505 (mm) REVERT: A 81 ASP cc_start: 0.8908 (t0) cc_final: 0.8511 (t0) REVERT: A 325 MET cc_start: 0.5719 (mmt) cc_final: 0.4538 (ptp) REVERT: C 80 GLU cc_start: 0.7877 (mp0) cc_final: 0.7522 (mp0) REVERT: C 81 ASP cc_start: 0.8938 (t0) cc_final: 0.8474 (t0) REVERT: C 204 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8891 (tt) REVERT: C 325 MET cc_start: 0.5241 (mmt) cc_final: 0.4188 (ppp) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.2143 time to fit residues: 37.6261 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 : 1.191 ------------------------------------------------------------------------------- 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 466 GLU 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 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 71 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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** ** 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 = 0.3560 r_free = 0.3560 target = 0.131434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102226 restraints weight = 14545.270| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.66 r_work: 0.3035 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 11454 Z= 0.118 Angle : 0.524 5.813 15666 Z= 0.254 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.058 1827 Dihedral : 12.509 115.844 2292 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 1.91 (0.25), residues: 1260 helix: 2.07 (0.20), residues: 735 sheet: 0.74 (0.49), residues: 138 loop : -0.05 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.018 0.001 PHE B 65 TYR 0.032 0.002 TYR B 427 ARG 0.009 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 582) hydrogen bonds : angle 4.59415 ( 1701) covalent geometry : bond 0.00278 (11448) covalent geometry : angle 0.52395 (15666) Misc. bond : bond 0.07083 ( 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 125 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.166 Fit side-chains REVERT: B 81 ASP cc_start: 0.8868 (t0) cc_final: 0.8410 (t0) REVERT: B 275 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8474 (mm) REVERT: A 81 ASP cc_start: 0.8900 (t0) cc_final: 0.8462 (t0) REVERT: A 204 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (tt) REVERT: A 325 MET cc_start: 0.5691 (mmt) cc_final: 0.4538 (ptp) REVERT: A 417 ARG cc_start: 0.7050 (mtp-110) cc_final: 0.6432 (mtp85) REVERT: C 80 GLU cc_start: 0.7982 (mp0) cc_final: 0.7612 (mp0) REVERT: C 81 ASP cc_start: 0.8946 (t0) cc_final: 0.8445 (t0) REVERT: C 204 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8874 (tt) REVERT: C 325 MET cc_start: 0.5170 (mmt) cc_final: 0.4142 (ppp) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.2056 time to fit residues: 37.0329 Evaluate side-chains 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 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 466 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 204 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 22 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104337 restraints weight = 14501.479| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.58 r_work: 0.3063 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11454 Z= 0.108 Angle : 0.513 5.120 15666 Z= 0.250 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.057 1827 Dihedral : 12.210 113.155 2292 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.50 % Allowed : 13.88 % Favored : 84.62 % 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: 1.92 (0.25), residues: 1260 helix: 2.07 (0.20), residues: 753 sheet: 0.77 (0.52), residues: 120 loop : -0.10 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 355 HIS 0.002 0.001 HIS C 409 PHE 0.021 0.001 PHE C 65 TYR 0.032 0.001 TYR B 427 ARG 0.006 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 582) hydrogen bonds : angle 4.53204 ( 1701) covalent geometry : bond 0.00247 (11448) covalent geometry : angle 0.51271 (15666) Misc. bond : bond 0.06094 ( 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 117 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.273 Fit side-chains REVERT: B 81 ASP cc_start: 0.8808 (t0) cc_final: 0.8356 (t0) REVERT: B 275 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 81 ASP cc_start: 0.8885 (t0) cc_final: 0.8468 (t0) REVERT: A 204 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8861 (tt) REVERT: A 325 MET cc_start: 0.5604 (mmt) cc_final: 0.4506 (ptp) REVERT: C 80 GLU cc_start: 0.7906 (mp0) cc_final: 0.7563 (mp0) REVERT: C 81 ASP cc_start: 0.8950 (t0) cc_final: 0.8486 (t0) REVERT: C 204 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 325 MET cc_start: 0.5275 (mmt) cc_final: 0.4273 (ppp) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.2062 time to fit residues: 35.3732 Evaluate side-chains 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 204 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 0.0170 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103986 restraints weight = 14499.996| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.59 r_work: 0.3053 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 11454 Z= 0.114 Angle : 0.518 5.612 15666 Z= 0.253 Chirality : 0.042 0.136 1737 Planarity : 0.005 0.080 1827 Dihedral : 12.100 111.757 2292 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.59 % Allowed : 13.88 % Favored : 84.53 % 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: 1.91 (0.25), residues: 1260 helix: 2.05 (0.20), residues: 753 sheet: 0.83 (0.52), residues: 120 loop : -0.10 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.030 0.001 PHE B 65 TYR 0.031 0.001 TYR B 427 ARG 0.007 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 582) hydrogen bonds : angle 4.53869 ( 1701) covalent geometry : bond 0.00267 (11448) covalent geometry : angle 0.51800 (15666) Misc. bond : bond 0.06125 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5299.37 seconds wall clock time: 91 minutes 50.66 seconds (5510.66 seconds total)