Starting phenix.real_space_refine on Wed Aug 5 20:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm4_37640/08_2026/8wm4_37640.map" } resolution = 2.93 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= 0.001 sd= 0.025 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 4 6.06 5 P 38 5.49 5 S 53 5.16 5 C 7151 2.51 5 N 2037 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11530 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10722 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 75, 'TRANS': 1255} Chain breaks: 11 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 804 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 704 SG CYS A 86 38.454 69.978 17.430 1.00163.97 S ATOM 950 SG CYS A 115 37.638 71.529 14.053 1.00166.94 S ATOM 1012 SG CYS A 123 35.076 71.742 16.908 1.00160.83 S ATOM 1036 SG CYS A 126 38.245 73.748 16.992 1.00162.01 S ATOM 3123 SG CYS A 463 47.884 48.549 43.963 1.00141.67 S ATOM 3221 SG CYS A 477 45.686 49.972 40.258 1.00100.77 S ATOM 5038 SG CYS A 706 59.479 38.249 68.581 1.00153.32 S ATOM 5053 SG CYS A 708 56.771 35.686 69.491 1.00124.76 S ATOM 5075 SG CYS A 711 55.779 39.247 68.454 1.00109.54 S ATOM 6938 SG CYS A 965 54.096 40.179 107.956 1.00 57.21 S ATOM 8561 SG CYS A1312 56.829 40.755 105.371 1.00112.45 S ATOM 8624 SG CYS A1342 55.453 37.220 106.081 1.00 60.94 S ATOM 8642 SG CYS A1345 53.393 39.494 104.170 1.00 93.73 S Time building chain proxies: 2.88, per 1000 atoms: 0.25 Number of scatterers: 11530 At special positions: 0 Unit cell: (78.2, 101.15, 171.7, 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 4 29.99 S 53 16.00 P 38 15.00 O 2247 8.00 N 2037 7.00 C 7151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 540.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " Number of angles added : 15 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 28.9% alpha, 15.7% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.282A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.808A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.255A pdb=" N ALA A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.864A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.681A pdb=" N LYS A 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 345 through 364 Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.835A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.033A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 648 Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.032A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.695A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.123A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 3.972A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 removed outlier: 3.778A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.206A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.956A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1593 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.769A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.518A pdb=" N HIS A 149 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 6.600A pdb=" N GLU A 403 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR A 579 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 405 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 577 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 407 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 575 " --> pdb=" O CYS A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 501 removed outlier: 3.921A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 521 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 517 " --> pdb=" O ARG A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.746A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.746A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 819 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 741 Processing sheet with id=AB3, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 867 Processing sheet with id=AB5, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB6, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.530A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 909 removed outlier: 3.773A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB9, first strand: chain 'A' and resid 1276 through 1280 removed outlier: 6.798A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1386 through 1387 342 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2883 1.33 - 1.46: 2714 1.46 - 1.58: 6120 1.58 - 1.70: 75 1.70 - 1.83: 76 Bond restraints: 11868 Sorted by residual: bond pdb=" N PRO A1253 " pdb=" CD PRO A1253 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" N VAL A1011 " pdb=" CA VAL A1011 " ideal model delta sigma weight residual 1.462 1.490 -0.028 8.70e-03 1.32e+04 1.05e+01 bond pdb=" N VAL A 817 " pdb=" CA VAL A 817 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.19e+00 bond pdb=" N GLU A1227 " pdb=" CA GLU A1227 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.66e+00 bond pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.59e+00 ... (remaining 11863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 15863 2.74 - 5.47: 250 5.47 - 8.21: 38 8.21 - 10.95: 11 10.95 - 13.68: 5 Bond angle restraints: 16167 Sorted by residual: angle pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " ideal model delta sigma weight residual 111.30 124.30 -13.00 2.30e+00 1.89e-01 3.20e+01 angle pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " pdb=" CD LYS A 297 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" N ASP A1298 " pdb=" CA ASP A1298 " pdb=" C ASP A1298 " ideal model delta sigma weight residual 113.97 107.10 6.87 1.28e+00 6.10e-01 2.88e+01 angle pdb=" CA TRP A1180 " pdb=" CB TRP A1180 " pdb=" CG TRP A1180 " ideal model delta sigma weight residual 113.60 122.66 -9.06 1.90e+00 2.77e-01 2.27e+01 angle pdb=" CA ILE A1236 " pdb=" CB ILE A1236 " pdb=" CG1 ILE A1236 " ideal model delta sigma weight residual 110.40 118.43 -8.03 1.70e+00 3.46e-01 2.23e+01 ... (remaining 16162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6236 17.87 - 35.75: 739 35.75 - 53.62: 195 53.62 - 71.50: 64 71.50 - 89.37: 21 Dihedral angle restraints: 7255 sinusoidal: 3430 harmonic: 3825 Sorted by residual: dihedral pdb=" CA TYR A1208 " pdb=" C TYR A1208 " pdb=" N TYR A1209 " pdb=" CA TYR A1209 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR A1217 " pdb=" C THR A1217 " pdb=" N PHE A1218 " pdb=" CA PHE A1218 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO A 198 " pdb=" C PRO A 198 " pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1448 0.067 - 0.134: 244 0.134 - 0.201: 27 0.201 - 0.268: 3 0.268 - 0.335: 5 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA ARG A 535 " pdb=" N ARG A 535 " pdb=" C ARG A 535 " pdb=" CB ARG A 535 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA MET A1211 " pdb=" N MET A1211 " pdb=" C MET A1211 " pdb=" CB MET A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LYS A1223 " pdb=" N LYS A1223 " pdb=" C LYS A1223 " pdb=" CB LYS A1223 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1724 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 20 " 0.018 2.00e-02 2.50e+03 2.39e-02 1.42e+01 pdb=" CG TRP A 20 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 20 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 20 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 20 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 20 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1439 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A1440 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1440 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1440 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 350 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" CD GLU A 350 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 350 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 350 " -0.018 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3100 2.81 - 3.33: 9309 3.33 - 3.86: 18342 3.86 - 4.38: 20769 4.38 - 4.90: 36164 Nonbonded interactions: 87684 Sorted by model distance: nonbonded pdb=" O THR A1185 " pdb=" OH TYR A1214 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLN A 21 " pdb=" CD2 PHE A 33 " model vdw 2.303 3.340 nonbonded pdb=" OG SER A 154 " pdb=" OP2 U R 0 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 863 " pdb=" OP2 A R 29 " model vdw 2.340 3.040 nonbonded pdb=" OD2 ASP A 193 " pdb=" OG1 THR A 195 " model vdw 2.360 3.040 ... (remaining 87679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.057 11882 Z= 0.234 Angle : 0.887 13.682 16182 Z= 0.502 Chirality : 0.053 0.335 1727 Planarity : 0.007 0.078 1963 Dihedral : 17.050 89.371 4787 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.78 % Allowed : 18.72 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.20), residues: 1307 helix: -0.78 (0.25), residues: 335 sheet: -0.23 (0.35), residues: 190 loop : -2.00 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 199 TYR 0.038 0.002 TYR A1228 PHE 0.028 0.002 PHE A 197 TRP 0.063 0.002 TRP A 20 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.23 (11868) covalent geometry : angle 0.88364 / 0.50 (16167) hydrogen bonds : bond 0.15850 / 10.59 ( 329) hydrogen bonds : angle 6.84900 / 5.07 ( 948) metal coordination : bond 0.00379 / 0.22 ( 14) metal coordination : angle 2.70513 / 1.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6726 (t-170) REVERT: A 199 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6653 (ttt-90) REVERT: A 236 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6124 (ttp-110) REVERT: A 771 MET cc_start: 0.6966 (mmm) cc_final: 0.6710 (mmm) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.6996 time to fit residues: 84.2042 Evaluate side-chains 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.185292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.140454 restraints weight = 15749.574| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.62 r_work: 0.4022 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11882 Z= 0.131 Angle : 0.587 7.638 16182 Z= 0.303 Chirality : 0.041 0.243 1727 Planarity : 0.005 0.054 1963 Dihedral : 13.944 92.431 2062 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.99 % Allowed : 19.32 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.40 (0.21), residues: 1307 helix: 0.40 (0.28), residues: 331 sheet: -0.10 (0.36), residues: 188 loop : -1.82 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 41 TYR 0.014 0.001 TYR A 190 PHE 0.013 0.001 PHE A1456 TRP 0.021 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11868) covalent geometry : angle 0.58273 / 0.30 (16167) hydrogen bonds : bond 0.04037 / 2.67 ( 329) hydrogen bonds : angle 5.15839 / 3.80 ( 948) metal coordination : bond 0.00674 / 0.34 ( 14) metal coordination : angle 2.46426 / 1.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6309 (mpp) REVERT: A 201 GLU cc_start: 0.5394 (mm-30) cc_final: 0.5139 (mm-30) REVERT: A 538 GLU cc_start: 0.6753 (tt0) cc_final: 0.6114 (mt-10) REVERT: A 581 ASP cc_start: 0.7759 (p0) cc_final: 0.7524 (m-30) REVERT: A 692 MET cc_start: 0.5132 (mmm) cc_final: 0.4347 (tmm) REVERT: A 827 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7429 (mptp) outliers start: 23 outliers final: 12 residues processed: 113 average time/residue: 0.5226 time to fit residues: 64.0542 Evaluate side-chains 101 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 0.0770 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 HIS A 816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.184204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.144781 restraints weight = 15797.187| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.79 r_work: 0.3983 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11882 Z= 0.099 Angle : 0.531 6.703 16182 Z= 0.271 Chirality : 0.039 0.140 1727 Planarity : 0.004 0.041 1963 Dihedral : 13.599 85.267 2049 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.65 % Allowed : 20.02 % Favored : 78.34 % 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: -1.05 (0.22), residues: 1307 helix: 0.87 (0.29), residues: 334 sheet: 0.04 (0.36), residues: 195 loop : -1.70 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 199 TYR 0.020 0.001 TYR A1228 PHE 0.009 0.001 PHE A1456 TRP 0.024 0.001 TRP A 20 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11868) covalent geometry : angle 0.52691 / 0.27 (16167) hydrogen bonds : bond 0.03347 / 2.20 ( 329) hydrogen bonds : angle 4.74008 / 3.49 ( 948) metal coordination : bond 0.00357 / 0.18 ( 14) metal coordination : angle 2.24199 / 1.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.297 Fit side-chains REVERT: A 6 LYS cc_start: 0.7509 (mppt) cc_final: 0.6863 (mtpt) REVERT: A 19 LYS cc_start: 0.5995 (pptt) cc_final: 0.5775 (mttp) REVERT: A 184 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7086 (t-170) REVERT: A 201 GLU cc_start: 0.5505 (mm-30) cc_final: 0.5269 (mm-30) REVERT: A 538 GLU cc_start: 0.6755 (tt0) cc_final: 0.6150 (mt-10) REVERT: A 593 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7867 (pttt) REVERT: A 827 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7504 (mptp) REVERT: A 1162 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.5475 (mttm) REVERT: A 1403 SER cc_start: 0.8180 (m) cc_final: 0.7734 (t) outliers start: 19 outliers final: 8 residues processed: 105 average time/residue: 0.5474 time to fit residues: 62.1360 Evaluate side-chains 98 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1432 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 816 GLN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.179658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.139802 restraints weight = 15756.357| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.66 r_work: 0.3930 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11882 Z= 0.157 Angle : 0.594 8.708 16182 Z= 0.301 Chirality : 0.042 0.307 1727 Planarity : 0.005 0.061 1963 Dihedral : 13.676 84.579 2049 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.69 % Allowed : 20.71 % Favored : 76.60 % 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: -1.05 (0.22), residues: 1307 helix: 0.97 (0.29), residues: 334 sheet: -0.12 (0.36), residues: 209 loop : -1.72 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 44 TYR 0.018 0.002 TYR A 958 PHE 0.018 0.002 PHE A1456 TRP 0.049 0.002 TRP A 315 HIS 0.008 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (11868) covalent geometry : angle 0.58757 / 0.30 (16167) hydrogen bonds : bond 0.04022 / 2.64 ( 329) hydrogen bonds : angle 4.81686 / 3.53 ( 948) metal coordination : bond 0.00478 / 0.25 ( 14) metal coordination : angle 2.88941 / 1.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.494 Fit side-chains REVERT: A 6 LYS cc_start: 0.7740 (mppt) cc_final: 0.7062 (mtpt) REVERT: A 184 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7059 (t70) REVERT: A 201 GLU cc_start: 0.5639 (mm-30) cc_final: 0.5409 (mm-30) REVERT: A 538 GLU cc_start: 0.6910 (tt0) cc_final: 0.6268 (mt-10) REVERT: A 692 MET cc_start: 0.5414 (mmm) cc_final: 0.4102 (tmm) REVERT: A 827 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7603 (mptp) REVERT: A 1162 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5409 (mttm) REVERT: A 1395 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7315 (mmm160) REVERT: A 1564 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7019 (tp) outliers start: 31 outliers final: 15 residues processed: 118 average time/residue: 0.5723 time to fit residues: 73.4247 Evaluate side-chains 111 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1432 THR Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 119 optimal weight: 0.2980 chunk 10 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 91 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.181401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.139896 restraints weight = 15633.359| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.66 r_work: 0.3968 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11882 Z= 0.103 Angle : 0.535 6.833 16182 Z= 0.273 Chirality : 0.039 0.198 1727 Planarity : 0.004 0.056 1963 Dihedral : 13.585 84.058 2049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.34 % Allowed : 21.49 % Favored : 76.17 % 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: -0.81 (0.22), residues: 1307 helix: 1.30 (0.30), residues: 328 sheet: 0.23 (0.37), residues: 188 loop : -1.64 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.016 0.001 TYR A1283 PHE 0.013 0.001 PHE A 237 TRP 0.054 0.001 TRP A 315 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (11868) covalent geometry : angle 0.52983 / 0.27 (16167) hydrogen bonds : bond 0.03281 / 2.15 ( 329) hydrogen bonds : angle 4.59601 / 3.39 ( 948) metal coordination : bond 0.00422 / 0.21 ( 14) metal coordination : angle 2.52527 / 1.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.422 Fit side-chains REVERT: A 6 LYS cc_start: 0.7629 (mppt) cc_final: 0.6952 (mtpt) REVERT: A 62 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.5056 (mmm-85) REVERT: A 184 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6995 (t70) REVERT: A 201 GLU cc_start: 0.5706 (mm-30) cc_final: 0.5467 (mm-30) REVERT: A 315 TRP cc_start: 0.6808 (m-10) cc_final: 0.6422 (m-10) REVERT: A 538 GLU cc_start: 0.6794 (tt0) cc_final: 0.6284 (mt-10) REVERT: A 593 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7833 (pttt) REVERT: A 827 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7595 (mptp) REVERT: A 1162 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5411 (mttm) outliers start: 27 outliers final: 10 residues processed: 112 average time/residue: 0.5817 time to fit residues: 70.4510 Evaluate side-chains 104 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1432 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.180736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.141044 restraints weight = 16009.902| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.64 r_work: 0.3981 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11882 Z= 0.177 Angle : 0.606 7.554 16182 Z= 0.305 Chirality : 0.042 0.164 1727 Planarity : 0.005 0.055 1963 Dihedral : 13.686 83.733 2049 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.21 % Allowed : 20.62 % Favored : 76.17 % 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: -0.97 (0.22), residues: 1307 helix: 1.07 (0.29), residues: 329 sheet: 0.02 (0.36), residues: 198 loop : -1.68 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.018 0.002 TYR A1283 PHE 0.017 0.002 PHE A 416 TRP 0.036 0.002 TRP A 315 HIS 0.008 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (11868) covalent geometry : angle 0.58986 / 0.30 (16167) hydrogen bonds : bond 0.04024 / 2.62 ( 329) hydrogen bonds : angle 4.77582 / 3.50 ( 948) metal coordination : bond 0.01861 / 0.93 ( 14) metal coordination : angle 4.53783 / 2.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: A 6 LYS cc_start: 0.7730 (mppt) cc_final: 0.7051 (mtpt) REVERT: A 62 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5422 (mmm-85) REVERT: A 184 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6896 (t70) REVERT: A 201 GLU cc_start: 0.5774 (mm-30) cc_final: 0.5551 (mm-30) REVERT: A 315 TRP cc_start: 0.7086 (m-10) cc_final: 0.6511 (m-10) REVERT: A 538 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6261 (mt-10) REVERT: A 827 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7667 (mptp) REVERT: A 1162 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5547 (mttm) REVERT: A 1395 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7324 (mmm160) outliers start: 37 outliers final: 17 residues processed: 118 average time/residue: 0.5092 time to fit residues: 64.6804 Evaluate side-chains 108 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1432 THR Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.181586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.142765 restraints weight = 15860.757| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.66 r_work: 0.3993 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11882 Z= 0.118 Angle : 0.578 10.409 16182 Z= 0.287 Chirality : 0.041 0.330 1727 Planarity : 0.004 0.052 1963 Dihedral : 13.634 83.294 2049 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.17 % Allowed : 21.49 % Favored : 76.34 % 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: -0.85 (0.22), residues: 1307 helix: 1.25 (0.29), residues: 329 sheet: 0.08 (0.36), residues: 198 loop : -1.63 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.013 0.001 TYR A 958 PHE 0.012 0.001 PHE A1456 TRP 0.030 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11868) covalent geometry : angle 0.56547 / 0.29 (16167) hydrogen bonds : bond 0.03468 / 2.27 ( 329) hydrogen bonds : angle 4.67268 / 3.44 ( 948) metal coordination : bond 0.00719 / 0.36 ( 14) metal coordination : angle 3.92008 / 2.19 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.353 Fit side-chains REVERT: A 6 LYS cc_start: 0.7640 (mppt) cc_final: 0.6958 (mtpt) REVERT: A 62 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5645 (mmm-85) REVERT: A 184 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6940 (t70) REVERT: A 201 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5653 (mm-30) REVERT: A 315 TRP cc_start: 0.7099 (m100) cc_final: 0.6508 (m-10) REVERT: A 538 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6230 (mt-10) REVERT: A 692 MET cc_start: 0.5206 (mmm) cc_final: 0.4163 (tmm) REVERT: A 827 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7637 (mptp) REVERT: A 1162 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.5528 (mttm) REVERT: A 1395 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7221 (mmm160) outliers start: 25 outliers final: 14 residues processed: 112 average time/residue: 0.5384 time to fit residues: 65.1392 Evaluate side-chains 105 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1432 THR Chi-restraints excluded: chain A residue 1544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 0.0030 chunk 109 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN A1186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.182839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.143843 restraints weight = 15836.382| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.70 r_work: 0.4022 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11882 Z= 0.101 Angle : 0.554 10.485 16182 Z= 0.278 Chirality : 0.040 0.314 1727 Planarity : 0.004 0.050 1963 Dihedral : 13.577 83.022 2049 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.34 % Allowed : 21.66 % Favored : 76.00 % 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: -0.74 (0.22), residues: 1307 helix: 1.35 (0.30), residues: 329 sheet: 0.17 (0.36), residues: 198 loop : -1.58 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.012 0.001 TYR A1283 PHE 0.017 0.001 PHE A 237 TRP 0.033 0.001 TRP A 20 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (11868) covalent geometry : angle 0.54485 / 0.28 (16167) hydrogen bonds : bond 0.03196 / 2.09 ( 329) hydrogen bonds : angle 4.57191 / 3.36 ( 948) metal coordination : bond 0.00589 / 0.29 ( 14) metal coordination : angle 3.39185 / 1.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.429 Fit side-chains REVERT: A 6 LYS cc_start: 0.7613 (mppt) cc_final: 0.6908 (mtpt) REVERT: A 62 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5622 (mmm-85) REVERT: A 184 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6896 (t70) REVERT: A 201 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5595 (mm-30) REVERT: A 315 TRP cc_start: 0.7054 (m100) cc_final: 0.6419 (m-10) REVERT: A 538 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6267 (mt-10) REVERT: A 593 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7978 (pttm) REVERT: A 692 MET cc_start: 0.5012 (mmm) cc_final: 0.4030 (tmm) REVERT: A 771 MET cc_start: 0.6860 (mmm) cc_final: 0.6650 (mmm) REVERT: A 827 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7653 (mptp) REVERT: A 1162 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5462 (mttm) REVERT: A 1208 TYR cc_start: 0.3911 (m-80) cc_final: 0.3568 (m-80) REVERT: A 1395 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7181 (mmm160) outliers start: 27 outliers final: 15 residues processed: 113 average time/residue: 0.5643 time to fit residues: 68.9021 Evaluate side-chains 109 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.179707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.136213 restraints weight = 15758.483| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.63 r_work: 0.3987 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11882 Z= 0.171 Angle : 0.626 9.423 16182 Z= 0.314 Chirality : 0.042 0.281 1727 Planarity : 0.005 0.050 1963 Dihedral : 13.688 83.098 2049 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.51 % Allowed : 21.92 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1307 helix: 1.11 (0.29), residues: 330 sheet: 0.11 (0.36), residues: 202 loop : -1.65 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 199 TYR 0.022 0.002 TYR A1228 PHE 0.021 0.002 PHE A 570 TRP 0.035 0.002 TRP A 20 HIS 0.009 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (11868) covalent geometry : angle 0.61593 / 0.31 (16167) hydrogen bonds : bond 0.03898 / 2.53 ( 329) hydrogen bonds : angle 4.78888 / 3.51 ( 948) metal coordination : bond 0.00599 / 0.32 ( 14) metal coordination : angle 3.63901 / 2.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.412 Fit side-chains REVERT: A 6 LYS cc_start: 0.7622 (mppt) cc_final: 0.6943 (mtpt) REVERT: A 62 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5762 (mmm-85) REVERT: A 184 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6718 (t70) REVERT: A 201 GLU cc_start: 0.5915 (mm-30) cc_final: 0.5657 (mm-30) REVERT: A 315 TRP cc_start: 0.7227 (m100) cc_final: 0.6543 (m-10) REVERT: A 538 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: A 827 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7678 (mptp) REVERT: A 1162 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5491 (mttm) REVERT: A 1395 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7254 (mmm160) outliers start: 29 outliers final: 19 residues processed: 108 average time/residue: 0.5886 time to fit residues: 68.6499 Evaluate side-chains 112 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.179321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.138923 restraints weight = 15932.045| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.60 r_work: 0.3986 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11882 Z= 0.168 Angle : 0.639 11.190 16182 Z= 0.320 Chirality : 0.043 0.275 1727 Planarity : 0.005 0.050 1963 Dihedral : 13.723 82.969 2049 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.25 % Allowed : 22.36 % Favored : 75.39 % 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: -0.97 (0.22), residues: 1307 helix: 1.02 (0.29), residues: 330 sheet: 0.06 (0.36), residues: 202 loop : -1.68 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.016 0.002 TYR A1283 PHE 0.020 0.002 PHE A 237 TRP 0.037 0.002 TRP A 20 HIS 0.008 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (11868) covalent geometry : angle 0.62980 / 0.32 (16167) hydrogen bonds : bond 0.03949 / 2.56 ( 329) hydrogen bonds : angle 4.84718 / 3.55 ( 948) metal coordination : bond 0.00592 / 0.31 ( 14) metal coordination : angle 3.58582 / 2.13 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.425 Fit side-chains REVERT: A 6 LYS cc_start: 0.7674 (mppt) cc_final: 0.6952 (mtpt) REVERT: A 62 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5875 (mmm-85) REVERT: A 184 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6729 (t70) REVERT: A 201 GLU cc_start: 0.5949 (mm-30) cc_final: 0.5651 (mm-30) REVERT: A 315 TRP cc_start: 0.7244 (m100) cc_final: 0.6537 (m-10) REVERT: A 538 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6315 (mt-10) REVERT: A 692 MET cc_start: 0.4777 (mmm) cc_final: 0.4478 (ptt) REVERT: A 827 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7679 (mptp) REVERT: A 1162 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5480 (mttm) REVERT: A 1395 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7203 (mmm160) outliers start: 26 outliers final: 18 residues processed: 111 average time/residue: 0.5198 time to fit residues: 62.6958 Evaluate side-chains 110 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 111 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.179789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.140557 restraints weight = 15989.434| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.81 r_work: 0.3987 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 11882 Z= 0.185 Angle : 0.885 59.199 16182 Z= 0.492 Chirality : 0.042 0.266 1727 Planarity : 0.005 0.050 1963 Dihedral : 13.722 82.945 2049 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.17 % Allowed : 22.44 % Favored : 75.39 % Cbeta Deviations : 0.08 % 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: -0.97 (0.22), residues: 1307 helix: 1.03 (0.29), residues: 330 sheet: 0.07 (0.36), residues: 202 loop : -1.68 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.015 0.002 TYR A 958 PHE 0.016 0.002 PHE A 570 TRP 0.033 0.002 TRP A 20 HIS 0.007 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (11868) covalent geometry : angle 0.87825 / 0.49 (16167) hydrogen bonds : bond 0.03869 / 2.51 ( 329) hydrogen bonds : angle 4.84131 / 3.54 ( 948) metal coordination : bond 0.00554 / 0.29 ( 14) metal coordination : angle 3.57050 / 2.12 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.00 seconds wall clock time: 63 minutes 48.75 seconds (3828.75 seconds total)