Starting phenix.real_space_refine on Wed Mar 4 17:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105.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 { model { file = "/net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg4_31105/03_2026/7eg4_31105.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 C 9770 2.51 5 N 2582 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15258 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'J36': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS D 277 24.703 60.259 74.608 1.00 63.56 S ATOM 5495 SG CYS D 311 25.288 59.169 77.864 1.00 50.53 S ATOM 5501 SG CYS D 312 28.122 61.185 76.154 1.00 45.94 S Restraints were copied for chains: A, B Time building chain proxies: 5.34, per 1000 atoms: 0.35 Number of scatterers: 15258 At special positions: 0 Unit cell: (100.672, 135.312, 128.817, 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) Zn 2 29.99 S 98 16.00 Mg 4 11.99 O 2802 8.00 N 2582 7.00 C 9770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 648.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 48.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 695 through 703 Processing helix chain 'C' and resid 709 through 723 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 731 through 746 Processing helix chain 'C' and resid 753 through 769 Processing helix chain 'C' and resid 816 through 821 removed outlier: 3.898A pdb=" N ASN C 820 " --> pdb=" O CYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 835 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 853 through 858 Processing helix chain 'C' and resid 863 through 880 removed outlier: 4.250A pdb=" N ARG C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 907 Processing helix chain 'C' and resid 908 through 911 removed outlier: 6.447A pdb=" N LYS C 911 " --> pdb=" O THR C 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 908 through 911' Processing helix chain 'C' and resid 912 through 925 Processing helix chain 'C' and resid 934 through 951 removed outlier: 3.789A pdb=" N ILE C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 956 Processing helix chain 'C' and resid 957 through 981 Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1008 through 1019 removed outlier: 3.520A pdb=" N ALA C1019 " --> pdb=" O SER C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1102 Processing helix chain 'D' and resid 24 through 31 Processing helix chain 'D' and resid 33 through 54 Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.550A pdb=" N THR D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.837A pdb=" N MET D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 232 removed outlier: 3.603A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 256 through 270 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 350 through 359 Processing helix chain 'D' and resid 394 through 402 removed outlier: 3.737A pdb=" N GLN D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.205A pdb=" N LYS D 407 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.915A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE D 524 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.629A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 731 through 746 Processing helix chain 'A' and resid 753 through 769 Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.898A pdb=" N ASN A 820 " --> pdb=" O CYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 863 through 880 removed outlier: 4.250A pdb=" N ARG A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 908 through 911 removed outlier: 6.446A pdb=" N LYS A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 908 through 911' Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 934 through 951 removed outlier: 3.789A pdb=" N ILE A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 957 through 981 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'A' and resid 1008 through 1019 removed outlier: 3.519A pdb=" N ALA A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1102 Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.550A pdb=" N THR B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.837A pdb=" N MET B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.603A pdb=" N ILE B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.737A pdb=" N GLN B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.205A pdb=" N LYS B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.914A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.629A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AA2, first strand: chain 'C' and resid 1025 through 1026 Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.736A pdb=" N SER D 4 " --> pdb=" O ASP D 17 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 16 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU D 62 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL D 18 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'D' and resid 171 through 172 removed outlier: 6.225A pdb=" N LEU B 16 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU B 62 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL B 18 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 4 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 204 through 207 removed outlier: 4.933A pdb=" N GLY D 300 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 292 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'D' and resid 440 through 443 removed outlier: 7.042A pdb=" N PHE D 458 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 443 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR D 456 " --> pdb=" O ASP D 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 772 through 773 Processing sheet with id=AB1, first strand: chain 'A' and resid 1025 through 1026 Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AB3, first strand: chain 'B' and resid 204 through 207 removed outlier: 4.933A pdb=" N GLY B 300 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 292 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AB5, first strand: chain 'B' and resid 440 through 443 removed outlier: 7.043A pdb=" N PHE B 458 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 443 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B 456 " --> pdb=" O ASP B 443 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4903 1.34 - 1.46: 2841 1.46 - 1.57: 7704 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 15598 Sorted by residual: bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" N GLU B 345 " pdb=" CA GLU B 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" C GLU B 393 " pdb=" N ASN B 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C GLU D 393 " pdb=" N ASN D 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C10 J36 C1201 " pdb=" C8 J36 C1201 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 15593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 19662 1.27 - 2.55: 1165 2.55 - 3.82: 182 3.82 - 5.09: 39 5.09 - 6.37: 16 Bond angle restraints: 21064 Sorted by residual: angle pdb=" C PRO B 502 " pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 122.35 128.23 -5.88 1.46e+00 4.69e-01 1.62e+01 angle pdb=" C PRO D 502 " pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 122.35 128.21 -5.86 1.46e+00 4.69e-01 1.61e+01 angle pdb=" N ASP B 546 " pdb=" CA ASP B 546 " pdb=" C ASP B 546 " ideal model delta sigma weight residual 114.56 110.28 4.28 1.27e+00 6.20e-01 1.14e+01 angle pdb=" N ASP D 546 " pdb=" CA ASP D 546 " pdb=" C ASP D 546 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" C TYR C 807 " pdb=" N ASN C 808 " pdb=" CA ASN C 808 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 21059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8466 17.99 - 35.97: 806 35.97 - 53.96: 120 53.96 - 71.95: 20 71.95 - 89.93: 16 Dihedral angle restraints: 9428 sinusoidal: 3912 harmonic: 5516 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 411 " pdb=" CB CYS B 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.11 -70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 381 " pdb=" SG CYS D 381 " pdb=" SG CYS D 411 " pdb=" CB CYS D 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.10 -70.10 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1407 0.037 - 0.074: 667 0.074 - 0.111: 159 0.111 - 0.148: 43 0.148 - 0.185: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA PRO D 382 " pdb=" N PRO D 382 " pdb=" C PRO D 382 " pdb=" CB PRO D 382 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 382 " pdb=" N PRO B 382 " pdb=" C PRO B 382 " pdb=" CB PRO B 382 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE D 550 " pdb=" N PHE D 550 " pdb=" C PHE D 550 " pdb=" CB PHE D 550 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2283 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 344 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ALA D 344 " 0.072 2.00e-02 2.50e+03 pdb=" O ALA D 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU D 345 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS C1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS C1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS C1088 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS A1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS A1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A1088 " -0.024 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 110 2.52 - 3.11: 12099 3.11 - 3.71: 21944 3.71 - 4.30: 32293 4.30 - 4.90: 55404 Nonbonded interactions: 121850 Sorted by model distance: nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 1.920 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 1.921 2.170 nonbonded pdb=" OG1 THR B 152 " pdb=" O GLY B 154 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR D 152 " pdb=" O GLY D 154 " model vdw 2.101 3.040 nonbonded pdb=" NE2 HIS C 836 " pdb="MG MG C1202 " model vdw 2.111 2.250 ... (remaining 121845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'D' 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.860 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 0.308 15610 Z= 0.502 Angle : 0.730 19.873 21074 Z= 0.404 Chirality : 0.045 0.185 2286 Planarity : 0.005 0.048 2694 Dihedral : 14.251 89.934 5854 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.17), residues: 1862 helix: -0.69 (0.16), residues: 854 sheet: -2.53 (0.35), residues: 166 loop : -3.54 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 387 TYR 0.022 0.002 TYR D 70 PHE 0.030 0.002 PHE D 550 TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00823 (15598) covalent geometry : angle 0.69891 (21064) SS BOND : bond 0.00060 ( 2) SS BOND : angle 3.12884 ( 4) hydrogen bonds : bond 0.16471 ( 682) hydrogen bonds : angle 5.69492 ( 1986) metal coordination : bond 0.08846 ( 8) metal coordination : angle 12.21066 ( 6) Misc. bond : bond 0.30801 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: C 923 LYS cc_start: 0.7435 (ttmt) cc_final: 0.7231 (ttmm) REVERT: C 1022 MET cc_start: 0.8710 (tpp) cc_final: 0.8146 (mmt) REVERT: D 48 MET cc_start: 0.8793 (ttt) cc_final: 0.8405 (ttt) REVERT: D 137 MET cc_start: 0.8948 (mtt) cc_final: 0.8668 (mtt) REVERT: D 221 ILE cc_start: 0.8439 (tp) cc_final: 0.7994 (pt) REVERT: D 377 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8212 (tp-100) REVERT: A 878 MET cc_start: 0.8331 (mtt) cc_final: 0.7933 (mtt) REVERT: A 923 LYS cc_start: 0.7475 (ttmt) cc_final: 0.7233 (ttmm) REVERT: A 1022 MET cc_start: 0.8401 (tpp) cc_final: 0.8049 (mmt) REVERT: B 48 MET cc_start: 0.8825 (ttt) cc_final: 0.8561 (ttt) REVERT: B 216 GLN cc_start: 0.6429 (tm-30) cc_final: 0.5410 (tt0) REVERT: B 265 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8052 (tp30) REVERT: B 341 MET cc_start: 0.8587 (mmm) cc_final: 0.8377 (mmt) REVERT: B 352 TYR cc_start: 0.7950 (t80) cc_final: 0.7743 (t80) REVERT: B 369 TRP cc_start: 0.8154 (m-90) cc_final: 0.7908 (m-90) REVERT: B 494 MET cc_start: 0.8451 (mmt) cc_final: 0.8210 (mmt) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1452 time to fit residues: 47.4581 Evaluate side-chains 153 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 713 GLN C 936 ASN C1081 GLN C1094 GLN D 41 ASN D 172 GLN D 284 ASN D 327 ASN D 360 ASN D 509 GLN D 553 ASN A 713 GLN A 936 ASN A1081 GLN B 41 ASN B 172 GLN B 284 ASN B 327 ASN B 360 ASN B 377 GLN B 509 GLN B 553 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102578 restraints weight = 21531.139| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.42 r_work: 0.3049 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15610 Z= 0.126 Angle : 0.575 11.332 21074 Z= 0.302 Chirality : 0.041 0.179 2286 Planarity : 0.005 0.055 2694 Dihedral : 4.524 26.366 2074 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.67 % Allowed : 8.91 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1862 helix: 0.75 (0.17), residues: 876 sheet: -1.91 (0.39), residues: 162 loop : -3.05 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 387 TYR 0.031 0.001 TYR D 301 PHE 0.032 0.001 PHE D 550 TRP 0.007 0.001 TRP D 110 HIS 0.002 0.001 HIS C1078 Details of bonding type rmsd covalent geometry : bond 0.00281 (15598) covalent geometry : angle 0.57341 (21064) SS BOND : bond 0.00784 ( 2) SS BOND : angle 1.39145 ( 4) hydrogen bonds : bond 0.03777 ( 682) hydrogen bonds : angle 4.03181 ( 1986) metal coordination : bond 0.01227 ( 8) metal coordination : angle 2.20288 ( 6) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.654 Fit side-chains REVERT: C 837 ASP cc_start: 0.8650 (m-30) cc_final: 0.8436 (m-30) REVERT: C 923 LYS cc_start: 0.7373 (ttmt) cc_final: 0.7020 (ttmm) REVERT: C 1094 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8360 (mm-40) REVERT: C 1095 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6470 (ttp-170) REVERT: D 48 MET cc_start: 0.9098 (ttt) cc_final: 0.8813 (ttt) REVERT: D 137 MET cc_start: 0.9363 (mtt) cc_final: 0.9076 (mtt) REVERT: D 177 MET cc_start: 0.8758 (mtm) cc_final: 0.8450 (mtp) REVERT: D 200 GLU cc_start: 0.8562 (pt0) cc_final: 0.8204 (pt0) REVERT: D 341 MET cc_start: 0.8801 (mmm) cc_final: 0.8427 (mmt) REVERT: A 923 LYS cc_start: 0.7488 (ttmt) cc_final: 0.7024 (ttmm) REVERT: A 1022 MET cc_start: 0.8664 (tpp) cc_final: 0.8230 (mmt) REVERT: B 369 TRP cc_start: 0.8016 (m-90) cc_final: 0.7690 (m-90) REVERT: B 393 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6715 (mm-30) outliers start: 28 outliers final: 15 residues processed: 193 average time/residue: 0.1459 time to fit residues: 41.1453 Evaluate side-chains 167 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 HIS ** C1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 41 ASN B 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.101825 restraints weight = 21969.470| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.46 r_work: 0.3039 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15610 Z= 0.139 Angle : 0.542 7.311 21074 Z= 0.286 Chirality : 0.041 0.181 2286 Planarity : 0.004 0.058 2694 Dihedral : 4.332 26.507 2074 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.03 % Allowed : 11.18 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1862 helix: 1.24 (0.17), residues: 876 sheet: -1.59 (0.39), residues: 164 loop : -2.77 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.011 0.001 TYR D 70 PHE 0.027 0.001 PHE B 550 TRP 0.007 0.001 TRP D 369 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00324 (15598) covalent geometry : angle 0.54010 (21064) SS BOND : bond 0.00074 ( 2) SS BOND : angle 1.04021 ( 4) hydrogen bonds : bond 0.03717 ( 682) hydrogen bonds : angle 3.87862 ( 1986) metal coordination : bond 0.00960 ( 8) metal coordination : angle 2.44039 ( 6) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: C 835 MET cc_start: 0.8444 (ptt) cc_final: 0.8191 (ptt) REVERT: C 923 LYS cc_start: 0.7544 (ttmt) cc_final: 0.7179 (ttmm) REVERT: C 1095 ARG cc_start: 0.6833 (ttm-80) cc_final: 0.6572 (ttp-170) REVERT: D 48 MET cc_start: 0.9136 (ttt) cc_final: 0.8861 (ttt) REVERT: D 137 MET cc_start: 0.9367 (mtt) cc_final: 0.9086 (mtt) REVERT: D 177 MET cc_start: 0.8802 (mtm) cc_final: 0.8491 (mtp) REVERT: D 195 LYS cc_start: 0.8650 (tptt) cc_final: 0.8408 (mmtm) REVERT: D 200 GLU cc_start: 0.8563 (pt0) cc_final: 0.8203 (pt0) REVERT: D 301 TYR cc_start: 0.8551 (m-80) cc_final: 0.8265 (m-10) REVERT: D 341 MET cc_start: 0.8834 (mmm) cc_final: 0.8482 (mmt) REVERT: D 377 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7950 (tp-100) REVERT: D 393 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6830 (mm-30) REVERT: A 923 LYS cc_start: 0.7476 (ttmt) cc_final: 0.7108 (ttmm) REVERT: B 200 GLU cc_start: 0.8311 (pt0) cc_final: 0.8027 (pt0) REVERT: B 369 TRP cc_start: 0.8012 (m-90) cc_final: 0.7775 (m-90) outliers start: 34 outliers final: 20 residues processed: 192 average time/residue: 0.1267 time to fit residues: 36.1408 Evaluate side-chains 170 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 30 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 41 ASN D 360 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 360 ASN B 553 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097085 restraints weight = 21858.292| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.45 r_work: 0.2975 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15610 Z= 0.277 Angle : 0.642 8.575 21074 Z= 0.337 Chirality : 0.046 0.233 2286 Planarity : 0.005 0.060 2694 Dihedral : 4.745 31.155 2074 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.63 % Allowed : 13.28 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1862 helix: 1.06 (0.17), residues: 872 sheet: -1.80 (0.36), residues: 186 loop : -2.74 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 155 TYR 0.013 0.002 TYR B 301 PHE 0.028 0.002 PHE B 550 TRP 0.010 0.002 TRP D 110 HIS 0.008 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00678 (15598) covalent geometry : angle 0.64065 (21064) SS BOND : bond 0.00803 ( 2) SS BOND : angle 1.10299 ( 4) hydrogen bonds : bond 0.04752 ( 682) hydrogen bonds : angle 4.04938 ( 1986) metal coordination : bond 0.00898 ( 8) metal coordination : angle 2.78238 ( 6) Misc. bond : bond 0.00101 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.645 Fit side-chains REVERT: C 923 LYS cc_start: 0.7514 (ttmt) cc_final: 0.7147 (ttmm) REVERT: C 997 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8892 (tp) REVERT: D 48 MET cc_start: 0.9190 (ttt) cc_final: 0.8925 (ttt) REVERT: D 137 MET cc_start: 0.9332 (mtt) cc_final: 0.9092 (mtt) REVERT: D 195 LYS cc_start: 0.8670 (tptt) cc_final: 0.8453 (mmtm) REVERT: D 200 GLU cc_start: 0.8607 (pt0) cc_final: 0.8298 (pt0) REVERT: D 301 TYR cc_start: 0.8513 (m-80) cc_final: 0.8235 (m-10) REVERT: D 341 MET cc_start: 0.8918 (mmm) cc_final: 0.8690 (mmt) REVERT: D 464 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: A 923 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7167 (ttmm) REVERT: A 935 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 280 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8340 (mmtm) REVERT: B 339 GLN cc_start: 0.8736 (tt0) cc_final: 0.8397 (mt0) REVERT: B 464 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: B 503 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6097 (pt0) REVERT: B 505 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5108 (mmp) outliers start: 44 outliers final: 30 residues processed: 188 average time/residue: 0.1274 time to fit residues: 35.8992 Evaluate side-chains 183 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN D 284 ASN D 360 ASN A 855 GLN B 41 ASN B 284 ASN B 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099309 restraints weight = 21514.059| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.45 r_work: 0.3009 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15610 Z= 0.182 Angle : 0.567 8.030 21074 Z= 0.298 Chirality : 0.042 0.210 2286 Planarity : 0.005 0.061 2694 Dihedral : 4.562 30.536 2074 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.11 % Allowed : 14.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1862 helix: 1.29 (0.17), residues: 878 sheet: -1.31 (0.39), residues: 164 loop : -2.64 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 709 TYR 0.012 0.001 TYR D 70 PHE 0.029 0.001 PHE B 550 TRP 0.008 0.001 TRP D 110 HIS 0.004 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00440 (15598) covalent geometry : angle 0.56538 (21064) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.94751 ( 4) hydrogen bonds : bond 0.04016 ( 682) hydrogen bonds : angle 3.87458 ( 1986) metal coordination : bond 0.00896 ( 8) metal coordination : angle 2.28788 ( 6) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: C 923 LYS cc_start: 0.7452 (ttmt) cc_final: 0.7091 (ttmm) REVERT: D 48 MET cc_start: 0.9213 (ttt) cc_final: 0.8922 (ttt) REVERT: D 137 MET cc_start: 0.9383 (mtt) cc_final: 0.9131 (mtt) REVERT: D 200 GLU cc_start: 0.8599 (pt0) cc_final: 0.8280 (pt0) REVERT: D 280 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8261 (mmtm) REVERT: D 301 TYR cc_start: 0.8424 (m-80) cc_final: 0.8220 (m-10) REVERT: D 341 MET cc_start: 0.8888 (mmm) cc_final: 0.8680 (mmt) REVERT: D 464 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: A 923 LYS cc_start: 0.7489 (ttmt) cc_final: 0.7042 (ttmm) REVERT: B 339 GLN cc_start: 0.8703 (tt0) cc_final: 0.8354 (mt0) REVERT: B 464 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7281 (mt-10) outliers start: 52 outliers final: 33 residues processed: 194 average time/residue: 0.1275 time to fit residues: 37.5564 Evaluate side-chains 181 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 112 optimal weight: 6.9990 chunk 127 optimal weight: 0.0570 chunk 179 optimal weight: 0.9990 chunk 130 optimal weight: 0.0060 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 855 GLN D 360 ASN D 380 HIS B 41 ASN B 284 ASN B 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102595 restraints weight = 21500.022| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.46 r_work: 0.3055 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15610 Z= 0.106 Angle : 0.511 8.926 21074 Z= 0.267 Chirality : 0.039 0.160 2286 Planarity : 0.004 0.061 2694 Dihedral : 4.262 28.028 2074 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.33 % Allowed : 15.01 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1862 helix: 1.79 (0.18), residues: 866 sheet: -1.06 (0.39), residues: 164 loop : -2.39 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.034 0.001 TYR B 301 PHE 0.027 0.001 PHE D 550 TRP 0.005 0.001 TRP A1026 HIS 0.003 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00236 (15598) covalent geometry : angle 0.51034 (21064) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.72833 ( 4) hydrogen bonds : bond 0.03197 ( 682) hydrogen bonds : angle 3.67584 ( 1986) metal coordination : bond 0.00634 ( 8) metal coordination : angle 1.89972 ( 6) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.656 Fit side-chains REVERT: C 923 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7069 (ttmm) REVERT: C 1085 MET cc_start: 0.8834 (ttp) cc_final: 0.8612 (ttp) REVERT: D 48 MET cc_start: 0.9090 (ttt) cc_final: 0.8803 (ttt) REVERT: D 137 MET cc_start: 0.9406 (mtt) cc_final: 0.9143 (mtt) REVERT: D 149 MET cc_start: 0.8474 (ttm) cc_final: 0.8258 (mtm) REVERT: D 195 LYS cc_start: 0.8761 (tptt) cc_final: 0.8541 (mmtm) REVERT: D 200 GLU cc_start: 0.8599 (pt0) cc_final: 0.8299 (pt0) REVERT: D 214 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6314 (mt) REVERT: D 301 TYR cc_start: 0.8405 (m-80) cc_final: 0.8110 (m-10) REVERT: D 341 MET cc_start: 0.8873 (mmm) cc_final: 0.8659 (mmt) REVERT: D 505 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5161 (mmp) REVERT: A 923 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7053 (ttmm) REVERT: B 149 MET cc_start: 0.8523 (ttm) cc_final: 0.8275 (mtm) REVERT: B 339 GLN cc_start: 0.8750 (tt0) cc_final: 0.8306 (mt0) REVERT: B 505 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.4955 (mmp) outliers start: 39 outliers final: 25 residues processed: 189 average time/residue: 0.1260 time to fit residues: 35.7926 Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 360 ASN B 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103473 restraints weight = 21379.274| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.46 r_work: 0.3071 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15610 Z= 0.103 Angle : 0.503 8.862 21074 Z= 0.263 Chirality : 0.039 0.185 2286 Planarity : 0.004 0.061 2694 Dihedral : 4.111 26.516 2074 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.15 % Allowed : 15.43 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1862 helix: 1.96 (0.18), residues: 866 sheet: -0.89 (0.40), residues: 164 loop : -2.25 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 526 TYR 0.012 0.001 TYR D 70 PHE 0.026 0.001 PHE D 550 TRP 0.004 0.001 TRP A 932 HIS 0.004 0.001 HIS C 868 Details of bonding type rmsd covalent geometry : bond 0.00233 (15598) covalent geometry : angle 0.50217 (21064) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.57410 ( 4) hydrogen bonds : bond 0.03069 ( 682) hydrogen bonds : angle 3.59817 ( 1986) metal coordination : bond 0.00714 ( 8) metal coordination : angle 1.97329 ( 6) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.672 Fit side-chains REVERT: C 923 LYS cc_start: 0.7374 (ttmt) cc_final: 0.7074 (ttmm) REVERT: D 48 MET cc_start: 0.9069 (ttt) cc_final: 0.8803 (ttt) REVERT: D 137 MET cc_start: 0.9395 (mtt) cc_final: 0.9157 (mtt) REVERT: D 149 MET cc_start: 0.8497 (ttm) cc_final: 0.8280 (mtm) REVERT: D 192 ARG cc_start: 0.7808 (tpt-90) cc_final: 0.7370 (ttt-90) REVERT: D 195 LYS cc_start: 0.8739 (tptt) cc_final: 0.8472 (mmtm) REVERT: D 200 GLU cc_start: 0.8559 (pt0) cc_final: 0.8231 (pt0) REVERT: D 214 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6292 (mt) REVERT: D 301 TYR cc_start: 0.8360 (m-80) cc_final: 0.8058 (m-10) REVERT: D 341 MET cc_start: 0.8866 (mmm) cc_final: 0.8656 (mmt) REVERT: D 464 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: D 505 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5058 (mmp) REVERT: A 923 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6970 (ttmm) REVERT: A 1095 ARG cc_start: 0.6807 (ttm-80) cc_final: 0.6481 (ttp-170) REVERT: B 149 MET cc_start: 0.8536 (ttm) cc_final: 0.8254 (mtm) REVERT: B 192 ARG cc_start: 0.7766 (tpt-90) cc_final: 0.7469 (ttt-90) REVERT: B 339 GLN cc_start: 0.8821 (tt0) cc_final: 0.8267 (mt0) REVERT: B 376 ARG cc_start: 0.6494 (ttm110) cc_final: 0.5898 (ttm-80) REVERT: B 464 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: B 505 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.4737 (mmp) outliers start: 36 outliers final: 23 residues processed: 189 average time/residue: 0.1198 time to fit residues: 34.3529 Evaluate side-chains 185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 53 optimal weight: 0.0020 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 44 optimal weight: 4.9990 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 868 HIS D 284 ASN D 360 ASN A 868 HIS A 913 HIS B 284 ASN B 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106031 restraints weight = 21782.319| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.56 r_work: 0.3106 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15610 Z= 0.093 Angle : 0.489 9.217 21074 Z= 0.254 Chirality : 0.039 0.166 2286 Planarity : 0.004 0.061 2694 Dihedral : 3.948 24.031 2074 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.97 % Allowed : 15.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1862 helix: 2.14 (0.18), residues: 866 sheet: -0.73 (0.41), residues: 164 loop : -2.15 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 526 TYR 0.009 0.001 TYR D 70 PHE 0.025 0.001 PHE B 550 TRP 0.007 0.001 TRP A 765 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00204 (15598) covalent geometry : angle 0.48772 (21064) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.51104 ( 4) hydrogen bonds : bond 0.02789 ( 682) hydrogen bonds : angle 3.51207 ( 1986) metal coordination : bond 0.00775 ( 8) metal coordination : angle 1.74682 ( 6) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.729 Fit side-chains REVERT: C 923 LYS cc_start: 0.7282 (ttmt) cc_final: 0.6991 (ttmm) REVERT: D 48 MET cc_start: 0.9049 (ttt) cc_final: 0.8839 (ttt) REVERT: D 137 MET cc_start: 0.9404 (mtt) cc_final: 0.9173 (mtt) REVERT: D 192 ARG cc_start: 0.7713 (tpt-90) cc_final: 0.7405 (ttt-90) REVERT: D 200 GLU cc_start: 0.8521 (pt0) cc_final: 0.8206 (pt0) REVERT: D 214 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6275 (mt) REVERT: D 341 MET cc_start: 0.8858 (mmm) cc_final: 0.8637 (mmt) REVERT: D 418 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7366 (mtp-110) REVERT: D 464 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: D 505 MET cc_start: 0.5680 (OUTLIER) cc_final: 0.4899 (mmp) REVERT: A 923 LYS cc_start: 0.7258 (ttmt) cc_final: 0.6920 (ttmm) REVERT: A 979 GLU cc_start: 0.8198 (tt0) cc_final: 0.7917 (tt0) REVERT: A 1095 ARG cc_start: 0.6740 (ttm-80) cc_final: 0.6403 (ttp-170) REVERT: B 149 MET cc_start: 0.8433 (ttm) cc_final: 0.8202 (mtm) REVERT: B 192 ARG cc_start: 0.7680 (tpt-90) cc_final: 0.7350 (ttt-90) REVERT: B 339 GLN cc_start: 0.8802 (tt0) cc_final: 0.8248 (mt0) REVERT: B 418 ARG cc_start: 0.8149 (mpp80) cc_final: 0.7473 (mtp-110) REVERT: B 464 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6108 (mp0) REVERT: B 505 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4381 (mmp) outliers start: 33 outliers final: 16 residues processed: 185 average time/residue: 0.1287 time to fit residues: 35.6801 Evaluate side-chains 175 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 5 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 284 ASN D 360 ASN B 284 ASN B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103389 restraints weight = 21631.452| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.49 r_work: 0.3061 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15610 Z= 0.118 Angle : 0.504 9.080 21074 Z= 0.263 Chirality : 0.040 0.170 2286 Planarity : 0.004 0.062 2694 Dihedral : 3.992 25.115 2074 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.73 % Allowed : 15.31 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1862 helix: 2.10 (0.18), residues: 866 sheet: -0.71 (0.41), residues: 164 loop : -2.11 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 709 TYR 0.011 0.001 TYR A 738 PHE 0.023 0.001 PHE B 550 TRP 0.006 0.001 TRP A 765 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00276 (15598) covalent geometry : angle 0.50289 (21064) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.55215 ( 4) hydrogen bonds : bond 0.03166 ( 682) hydrogen bonds : angle 3.55301 ( 1986) metal coordination : bond 0.00660 ( 8) metal coordination : angle 1.94876 ( 6) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.549 Fit side-chains REVERT: C 923 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6975 (ttmm) REVERT: D 48 MET cc_start: 0.9130 (ttt) cc_final: 0.8886 (ttt) REVERT: D 137 MET cc_start: 0.9395 (mtt) cc_final: 0.9168 (mtt) REVERT: D 192 ARG cc_start: 0.7798 (tpt-90) cc_final: 0.7518 (ttt-90) REVERT: D 195 LYS cc_start: 0.8727 (tptt) cc_final: 0.8087 (mmtm) REVERT: D 200 GLU cc_start: 0.8552 (pt0) cc_final: 0.8263 (pt0) REVERT: D 341 MET cc_start: 0.8866 (mmm) cc_final: 0.8662 (mmt) REVERT: D 376 ARG cc_start: 0.6353 (ttm170) cc_final: 0.5903 (ttp80) REVERT: D 418 ARG cc_start: 0.8113 (mpp80) cc_final: 0.7464 (mtp85) REVERT: D 464 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: D 505 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.4961 (mmp) REVERT: A 923 LYS cc_start: 0.7260 (ttmt) cc_final: 0.6931 (ttmm) REVERT: A 1095 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6416 (ttp-170) REVERT: B 192 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7441 (ttt-90) REVERT: B 339 GLN cc_start: 0.8817 (tt0) cc_final: 0.8263 (mt0) REVERT: B 418 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7465 (mtp-110) REVERT: B 464 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: B 505 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4307 (mmp) outliers start: 29 outliers final: 17 residues processed: 176 average time/residue: 0.1228 time to fit residues: 32.0491 Evaluate side-chains 168 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 284 ASN D 360 ASN B 284 ASN B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104045 restraints weight = 21759.879| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.49 r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15610 Z= 0.107 Angle : 0.512 10.089 21074 Z= 0.264 Chirality : 0.040 0.181 2286 Planarity : 0.004 0.062 2694 Dihedral : 4.004 25.205 2074 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.73 % Allowed : 15.49 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1862 helix: 2.14 (0.18), residues: 866 sheet: -0.64 (0.41), residues: 164 loop : -2.08 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 709 TYR 0.010 0.001 TYR D 70 PHE 0.024 0.001 PHE B 550 TRP 0.007 0.001 TRP A 765 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00249 (15598) covalent geometry : angle 0.51087 (21064) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.56168 ( 4) hydrogen bonds : bond 0.03024 ( 682) hydrogen bonds : angle 3.52364 ( 1986) metal coordination : bond 0.00683 ( 8) metal coordination : angle 1.94450 ( 6) Misc. bond : bond 0.00049 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.524 Fit side-chains REVERT: C 923 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6964 (ttmm) REVERT: D 48 MET cc_start: 0.9084 (ttt) cc_final: 0.8825 (ttt) REVERT: D 137 MET cc_start: 0.9393 (mtt) cc_final: 0.9172 (mtt) REVERT: D 192 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7528 (ttt-90) REVERT: D 195 LYS cc_start: 0.8723 (tptt) cc_final: 0.8081 (mmtm) REVERT: D 200 GLU cc_start: 0.8559 (pt0) cc_final: 0.8229 (pt0) REVERT: D 214 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6298 (mt) REVERT: D 221 ILE cc_start: 0.8314 (tp) cc_final: 0.7671 (pt) REVERT: D 373 GLU cc_start: 0.8839 (pt0) cc_final: 0.8527 (pm20) REVERT: D 376 ARG cc_start: 0.6391 (ttm170) cc_final: 0.5906 (ttp80) REVERT: D 418 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7445 (mtp85) REVERT: D 464 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: D 505 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.4951 (mmp) REVERT: A 923 LYS cc_start: 0.7246 (ttmt) cc_final: 0.6929 (ttmm) REVERT: A 1095 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.6389 (ttp-170) REVERT: B 192 ARG cc_start: 0.7760 (tpt-90) cc_final: 0.7483 (ttt-90) REVERT: B 339 GLN cc_start: 0.8813 (tt0) cc_final: 0.8251 (mt0) REVERT: B 376 ARG cc_start: 0.6453 (ttm110) cc_final: 0.5836 (ttm-80) REVERT: B 418 ARG cc_start: 0.8130 (mpp80) cc_final: 0.7433 (mtp-110) REVERT: B 464 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 505 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.4275 (mmp) outliers start: 29 outliers final: 21 residues processed: 171 average time/residue: 0.1278 time to fit residues: 32.6421 Evaluate side-chains 174 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 102 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.0070 chunk 18 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 284 ASN D 360 ASN B 284 ASN B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103219 restraints weight = 21606.464| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.48 r_work: 0.3059 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15610 Z= 0.118 Angle : 0.519 9.670 21074 Z= 0.267 Chirality : 0.040 0.163 2286 Planarity : 0.004 0.062 2694 Dihedral : 4.033 25.861 2074 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.73 % Allowed : 15.55 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1862 helix: 2.12 (0.18), residues: 866 sheet: -0.60 (0.41), residues: 164 loop : -2.08 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 709 TYR 0.010 0.001 TYR A 738 PHE 0.023 0.001 PHE B 550 TRP 0.006 0.001 TRP C1026 HIS 0.005 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00278 (15598) covalent geometry : angle 0.51785 (21064) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.59163 ( 4) hydrogen bonds : bond 0.03179 ( 682) hydrogen bonds : angle 3.55054 ( 1986) metal coordination : bond 0.00611 ( 8) metal coordination : angle 1.91029 ( 6) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.81 seconds wall clock time: 67 minutes 6.91 seconds (4026.91 seconds total)