Starting phenix.real_space_refine on Thu Jul 2 23:56:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2026/7ele_31182.cif" } resolution = 4.9 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= 0.002 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: 5 Type Number sf(0) Gaussians P 83 5.49 5 S 60 5.16 5 C 6512 2.51 5 N 1851 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10733 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8976 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 38, 'TRANS': 1098} Chain breaks: 12 Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1757 Classifications: {'RNA': 83} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 39, 'rna3p_pyr': 42} Link IDs: {'rna2p': 1, 'rna3p': 81} Chain breaks: 3 Time building chain proxies: 2.64, per 1000 atoms: 0.25 Number of scatterers: 10733 At special positions: 0 Unit cell: (161.226, 129.792, 93.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 83 15.00 O 2227 8.00 N 1851 7.00 C 6512 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: 1.02 Conformation dependent library (CDL) restraints added in 389.7 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 54.4% alpha, 6.6% beta 35 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.828A pdb=" N LEU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.055A pdb=" N ARG A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.739A pdb=" N ILE A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.887A pdb=" N LEU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 473 through 493 removed outlier: 3.912A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 567 removed outlier: 3.612A pdb=" N GLY A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N TRP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.752A pdb=" N GLU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 673 through 687 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 823 through 826 removed outlier: 3.956A pdb=" N TYR A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 827 through 849 removed outlier: 3.810A pdb=" N THR A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 1049 through 1066 Processing helix chain 'A' and resid 1103 through 1113 Processing helix chain 'A' and resid 1254 through 1264 Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 4.085A pdb=" N VAL A1307 " --> pdb=" O LYS A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1348 Proline residue: A1331 - end of helix removed outlier: 3.565A pdb=" N ASN A1348 " --> pdb=" O VAL A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1364 removed outlier: 3.508A pdb=" N THR A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1397 Processing helix chain 'A' and resid 1401 through 1413 Processing helix chain 'A' and resid 1414 through 1426 removed outlier: 3.589A pdb=" N LEU A1418 " --> pdb=" O SER A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1430 Processing helix chain 'A' and resid 1501 through 1517 removed outlier: 3.753A pdb=" N GLY A1517 " --> pdb=" O TYR A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1530 removed outlier: 3.740A pdb=" N ALA A1522 " --> pdb=" O GLY A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1566 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.696A pdb=" N LEU A1576 " --> pdb=" O GLU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1615 Processing helix chain 'A' and resid 1620 through 1632 Processing helix chain 'A' and resid 1633 through 1645 removed outlier: 3.548A pdb=" N PHE A1637 " --> pdb=" O ASN A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1668 removed outlier: 3.628A pdb=" N GLU A1658 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1668 " --> pdb=" O PHE A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1706 Processing helix chain 'A' and resid 1710 through 1722 removed outlier: 3.512A pdb=" N VAL A1716 " --> pdb=" O ALA A1712 " (cutoff:3.500A) Proline residue: A1719 - end of helix Processing helix chain 'A' and resid 1723 through 1725 No H-bonds generated for 'chain 'A' and resid 1723 through 1725' Processing helix chain 'A' and resid 1733 through 1742 Processing helix chain 'A' and resid 1781 through 1794 Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 302 removed outlier: 5.618A pdb=" N VAL A 300 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP A 378 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 302 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 375 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET A 411 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 377 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 265 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE A 266 " --> pdb=" O CYS A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 463 removed outlier: 5.835A pdb=" N SER A 459 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 773 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 461 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 745 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET A 774 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 668 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 667 " --> pdb=" O ALA A 729 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 862 through 867 Processing sheet with id=AA4, first strand: chain 'A' and resid 1026 through 1029 removed outlier: 4.882A pdb=" N SER A 979 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1011 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1086 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1308 through 1309 removed outlier: 6.431A pdb=" N LEU A1274 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A1230 " --> pdb=" O LEU A1274 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS A1276 " --> pdb=" O ASP A1228 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP A1228 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1211 " --> pdb=" O HIS A1317 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1315 " --> pdb=" O GLY A1213 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1869 1.33 - 1.45: 3078 1.45 - 1.57: 5886 1.57 - 1.69: 162 1.69 - 1.81: 96 Bond restraints: 11091 Sorted by residual: bond pdb=" N ILE A 693 " pdb=" CA ILE A 693 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" N VAL A 728 " pdb=" CA VAL A 728 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N ILE A 367 " pdb=" CA ILE A 367 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N VAL A 669 " pdb=" CA VAL A 669 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE A 858 " pdb=" CA ILE A 858 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 11086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14113 2.04 - 4.07: 1096 4.07 - 6.11: 114 6.11 - 8.14: 28 8.14 - 10.18: 7 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N LEU A1427 " pdb=" CA LEU A1427 " pdb=" C LEU A1427 " ideal model delta sigma weight residual 113.19 105.76 7.43 1.19e+00 7.06e-01 3.90e+01 angle pdb=" C4' U G 49 " pdb=" C3' U G 49 " pdb=" O3' U G 49 " ideal model delta sigma weight residual 113.00 121.48 -8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" N GLU A 799 " pdb=" CA GLU A 799 " pdb=" C GLU A 799 " ideal model delta sigma weight residual 112.89 106.12 6.77 1.24e+00 6.50e-01 2.98e+01 angle pdb=" N THR A1501 " pdb=" CA THR A1501 " pdb=" C THR A1501 " ideal model delta sigma weight residual 113.02 106.92 6.10 1.20e+00 6.94e-01 2.58e+01 angle pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" C THR A 412 " ideal model delta sigma weight residual 113.30 106.50 6.80 1.34e+00 5.57e-01 2.57e+01 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6197 35.91 - 71.82: 345 71.82 - 107.73: 14 107.73 - 143.65: 1 143.65 - 179.56: 3 Dihedral angle restraints: 6560 sinusoidal: 3234 harmonic: 3326 Sorted by residual: dihedral pdb=" CA GLN A1722 " pdb=" C GLN A1722 " pdb=" N PRO A1723 " pdb=" CA PRO A1723 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N CYS A 328 " pdb=" CA CYS A 328 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A1374 " pdb=" C TYR A1374 " pdb=" N GLU A1375 " pdb=" CA GLU A1375 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1537 0.087 - 0.173: 253 0.173 - 0.260: 38 0.260 - 0.346: 2 0.346 - 0.433: 1 Chirality restraints: 1831 Sorted by residual: chirality pdb=" C3' U G 49 " pdb=" C4' U G 49 " pdb=" O3' U G 49 " pdb=" C2' U G 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C2' G G 36 " pdb=" C3' G G 36 " pdb=" O2' G G 36 " pdb=" C1' G G 36 " both_signs ideal model delta sigma weight residual False -2.75 -2.43 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3' U G 25 " pdb=" C4' U G 25 " pdb=" O3' U G 25 " pdb=" C2' U G 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1828 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 663 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C ALA A 663 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 663 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 664 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 387 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 388 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1426 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLY A1426 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY A1426 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A1427 " -0.014 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1544 2.75 - 3.29: 11596 3.29 - 3.82: 21135 3.82 - 4.36: 24828 4.36 - 4.90: 34960 Nonbonded interactions: 94063 Sorted by model distance: nonbonded pdb=" O ALA A 789 " pdb=" OG SER A 792 " model vdw 2.210 3.040 nonbonded pdb=" O PHE A 846 " pdb=" OG SER A 849 " model vdw 2.222 3.040 nonbonded pdb=" O2 U G 26 " pdb=" N2 G G 62 " model vdw 2.231 2.496 nonbonded pdb=" O LEU A 391 " pdb=" OG SER A 394 " model vdw 2.238 3.040 nonbonded pdb=" O LEU A1301 " pdb=" OG1 THR A1304 " model vdw 2.239 3.040 ... (remaining 94058 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 group one per residue 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: 0.730 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: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.040 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: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.007 0.051 11091 Z= 0.457 Angle : 1.164 10.177 15358 Z= 0.721 Chirality : 0.065 0.433 1831 Planarity : 0.006 0.063 1638 Dihedral : 19.443 179.557 4400 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.09 % Favored : 90.10 % Rotamer: Outliers : 8.44 % Allowed : 13.63 % Favored : 77.92 % 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: -3.55 (0.21), residues: 1111 helix: -1.87 (0.18), residues: 568 sheet: -2.57 (0.51), residues: 75 loop : -2.84 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1391 TYR 0.021 0.003 TYR A 757 PHE 0.022 0.003 PHE A1392 TRP 0.018 0.003 TRP A 336 HIS 0.010 0.002 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.46 (11091) covalent geometry : angle 1.16387 / 0.72 (15358) hydrogen bonds : bond 0.14768 / 9.82 ( 521) hydrogen bonds : angle 8.00343 / 5.73 ( 1438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 122 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.9818 (mm-40) cc_final: 0.9533 (tp40) REVERT: A 331 MET cc_start: 0.7068 (mtp) cc_final: 0.6798 (mtm) REVERT: A 352 VAL cc_start: 0.9594 (t) cc_final: 0.9234 (m) REVERT: A 393 MET cc_start: 0.9478 (tpt) cc_final: 0.9058 (tpp) REVERT: A 397 TYR cc_start: 0.9695 (t80) cc_final: 0.9456 (t80) REVERT: A 670 PHE cc_start: 0.9605 (m-80) cc_final: 0.9271 (m-80) REVERT: A 691 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 746 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.9235 (tpp) REVERT: A 845 HIS cc_start: 0.9006 (t70) cc_final: 0.8764 (t70) REVERT: A 900 MET cc_start: 0.9432 (ttp) cc_final: 0.9207 (tpt) REVERT: A 1087 PHE cc_start: 0.9083 (m-10) cc_final: 0.8761 (p90) REVERT: A 1261 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 1408 MET cc_start: 0.9507 (mmm) cc_final: 0.9254 (mtt) REVERT: A 1416 MET cc_start: 0.9634 (mmt) cc_final: 0.9407 (mmp) REVERT: A 1742 CYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5279 (p) REVERT: A 1781 MET cc_start: 0.8569 (mmt) cc_final: 0.8322 (mmp) outliers start: 83 outliers final: 26 residues processed: 193 average time/residue: 0.1230 time to fit residues: 32.3239 Evaluate side-chains 115 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 532 HIS A 661 HIS A 713 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS A1411 GLN A1428 GLN A1523 ASN A1582 HIS ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN A1758 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.061602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048767 restraints weight = 150917.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049884 restraints weight = 104583.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050644 restraints weight = 80422.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051193 restraints weight = 66597.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.051602 restraints weight = 57856.865| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11091 Z= 0.167 Angle : 0.749 10.617 15358 Z= 0.388 Chirality : 0.042 0.256 1831 Planarity : 0.006 0.072 1638 Dihedral : 15.720 177.848 2210 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.53 % Rotamer: Outliers : 0.61 % Allowed : 7.12 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.47 (0.23), residues: 1111 helix: -0.77 (0.20), residues: 576 sheet: -2.65 (0.44), residues: 104 loop : -2.49 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 666 TYR 0.038 0.002 TYR A 757 PHE 0.020 0.002 PHE A1225 TRP 0.044 0.003 TRP A 341 HIS 0.005 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (11091) covalent geometry : angle 0.74921 / 0.39 (15358) hydrogen bonds : bond 0.06726 / 4.45 ( 521) hydrogen bonds : angle 6.18379 / 4.48 ( 1438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9104 (mp0) REVERT: A 393 MET cc_start: 0.9159 (tpt) cc_final: 0.8377 (tpp) REVERT: A 411 MET cc_start: 0.6963 (mtt) cc_final: 0.6599 (mtt) REVERT: A 746 MET cc_start: 0.9457 (tpt) cc_final: 0.8598 (mmm) REVERT: A 774 MET cc_start: 0.8660 (ttt) cc_final: 0.6527 (tpp) REVERT: A 1234 MET cc_start: 0.8821 (tpt) cc_final: 0.8423 (tpp) REVERT: A 1340 MET cc_start: 0.9011 (mmm) cc_final: 0.8551 (mmm) REVERT: A 1570 PHE cc_start: 0.5137 (t80) cc_final: 0.4650 (t80) REVERT: A 1576 LEU cc_start: 0.9581 (tt) cc_final: 0.9365 (tt) REVERT: A 1646 LEU cc_start: 0.9169 (mm) cc_final: 0.8612 (mm) outliers start: 6 outliers final: 1 residues processed: 114 average time/residue: 0.0894 time to fit residues: 15.0296 Evaluate side-chains 81 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.060965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048105 restraints weight = 152107.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.049208 restraints weight = 106224.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049961 restraints weight = 81748.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.050497 restraints weight = 67698.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050911 restraints weight = 58836.117| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11091 Z= 0.157 Angle : 0.701 10.821 15358 Z= 0.363 Chirality : 0.041 0.225 1831 Planarity : 0.005 0.069 1638 Dihedral : 15.281 172.879 2210 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.01 % Favored : 91.81 % Rotamer: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % 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: -2.24 (0.23), residues: 1111 helix: -0.48 (0.21), residues: 581 sheet: -2.38 (0.50), residues: 87 loop : -2.63 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1391 TYR 0.032 0.002 TYR A 757 PHE 0.031 0.002 PHE A 556 TRP 0.023 0.002 TRP A 341 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (11091) covalent geometry : angle 0.70077 / 0.36 (15358) hydrogen bonds : bond 0.06516 / 4.32 ( 521) hydrogen bonds : angle 5.91948 / 4.28 ( 1438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9189 (tpt) cc_final: 0.8516 (tpp) REVERT: A 746 MET cc_start: 0.9554 (tpt) cc_final: 0.8509 (mmm) REVERT: A 774 MET cc_start: 0.8567 (ttt) cc_final: 0.6810 (tpp) REVERT: A 1234 MET cc_start: 0.8879 (tpt) cc_final: 0.8673 (tpt) REVERT: A 1340 MET cc_start: 0.9185 (mmm) cc_final: 0.8739 (mmm) REVERT: A 1412 MET cc_start: 0.9403 (mmp) cc_final: 0.9100 (mmm) REVERT: A 1570 PHE cc_start: 0.5297 (t80) cc_final: 0.5093 (t80) REVERT: A 1576 LEU cc_start: 0.9571 (tt) cc_final: 0.9346 (tt) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.0937 time to fit residues: 13.9687 Evaluate side-chains 75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1428 GLN A1647 HIS A1758 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.063330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050307 restraints weight = 149198.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051472 restraints weight = 104382.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.052253 restraints weight = 80126.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.052785 restraints weight = 66245.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.053190 restraints weight = 57656.202| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11091 Z= 0.131 Angle : 0.659 11.456 15358 Z= 0.334 Chirality : 0.039 0.182 1831 Planarity : 0.004 0.047 1638 Dihedral : 14.551 165.549 2210 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.92 % Favored : 91.90 % Rotamer: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.24), residues: 1111 helix: -0.13 (0.21), residues: 583 sheet: -1.93 (0.53), residues: 87 loop : -2.59 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 405 TYR 0.026 0.001 TYR A 757 PHE 0.019 0.001 PHE A 556 TRP 0.016 0.002 TRP A 341 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11091) covalent geometry : angle 0.65889 / 0.33 (15358) hydrogen bonds : bond 0.06198 / 4.09 ( 521) hydrogen bonds : angle 5.55051 / 4.03 ( 1438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9195 (tpt) cc_final: 0.8524 (tpp) REVERT: A 746 MET cc_start: 0.9617 (tpt) cc_final: 0.8561 (mmm) REVERT: A 1340 MET cc_start: 0.9175 (mmm) cc_final: 0.8756 (mmm) REVERT: A 1412 MET cc_start: 0.9439 (mmp) cc_final: 0.9134 (mmm) REVERT: A 1570 PHE cc_start: 0.5540 (t80) cc_final: 0.5312 (t80) REVERT: A 1646 LEU cc_start: 0.9220 (mm) cc_final: 0.8676 (mm) REVERT: A 1758 ASN cc_start: 0.5713 (OUTLIER) cc_final: 0.5309 (m-40) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.0872 time to fit residues: 14.3611 Evaluate side-chains 80 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.1980 chunk 103 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 GLN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 GLN ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.046734 restraints weight = 151910.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047794 restraints weight = 109276.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048517 restraints weight = 85569.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.049033 restraints weight = 71541.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049432 restraints weight = 62601.698| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11091 Z= 0.186 Angle : 0.708 8.972 15358 Z= 0.366 Chirality : 0.041 0.209 1831 Planarity : 0.005 0.050 1638 Dihedral : 14.735 159.805 2210 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.91 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.24), residues: 1111 helix: -0.26 (0.20), residues: 589 sheet: -1.97 (0.53), residues: 82 loop : -2.55 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1391 TYR 0.020 0.002 TYR A 757 PHE 0.017 0.002 PHE A1225 TRP 0.013 0.002 TRP A1104 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (11091) covalent geometry : angle 0.70828 / 0.37 (15358) hydrogen bonds : bond 0.06824 / 4.53 ( 521) hydrogen bonds : angle 5.75294 / 4.16 ( 1438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9295 (tpt) cc_final: 0.8009 (tpp) REVERT: A 411 MET cc_start: 0.6893 (mtt) cc_final: 0.6436 (mtt) REVERT: A 746 MET cc_start: 0.9490 (tpt) cc_final: 0.9210 (tpp) REVERT: A 1340 MET cc_start: 0.9320 (mmm) cc_final: 0.8868 (mmm) REVERT: A 1412 MET cc_start: 0.9640 (mmp) cc_final: 0.9419 (mmm) REVERT: A 1576 LEU cc_start: 0.9698 (tt) cc_final: 0.9490 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0886 time to fit residues: 12.5334 Evaluate side-chains 70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 20 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.062018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.048928 restraints weight = 149849.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.050029 restraints weight = 106032.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050788 restraints weight = 82452.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051338 restraints weight = 68294.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.051758 restraints weight = 59317.405| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11091 Z= 0.141 Angle : 0.683 13.771 15358 Z= 0.345 Chirality : 0.040 0.188 1831 Planarity : 0.005 0.048 1638 Dihedral : 14.366 158.115 2210 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.92 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1111 helix: -0.01 (0.21), residues: 585 sheet: -1.95 (0.55), residues: 76 loop : -2.52 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1391 TYR 0.019 0.001 TYR A 757 PHE 0.014 0.001 PHE A 889 TRP 0.013 0.002 TRP A1104 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11091) covalent geometry : angle 0.68345 / 0.34 (15358) hydrogen bonds : bond 0.06381 / 4.23 ( 521) hydrogen bonds : angle 5.55845 / 4.02 ( 1438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 746 MET cc_start: 0.9580 (tpt) cc_final: 0.9137 (tpp) REVERT: A 843 LEU cc_start: 0.9347 (mm) cc_final: 0.9110 (tp) REVERT: A 1234 MET cc_start: 0.8716 (tpt) cc_final: 0.8374 (tpp) REVERT: A 1340 MET cc_start: 0.8976 (mmm) cc_final: 0.8624 (mmm) REVERT: A 1412 MET cc_start: 0.9444 (mmp) cc_final: 0.9118 (mmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0916 time to fit residues: 13.8348 Evaluate side-chains 76 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 15 optimal weight: 0.0980 chunk 65 optimal weight: 0.0040 chunk 70 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.061105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048045 restraints weight = 150842.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.049127 restraints weight = 107684.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.049862 restraints weight = 84004.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050398 restraints weight = 69866.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050813 restraints weight = 60862.914| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11091 Z= 0.150 Angle : 0.685 13.646 15358 Z= 0.348 Chirality : 0.040 0.184 1831 Planarity : 0.004 0.050 1638 Dihedral : 14.221 158.269 2210 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -1.67 (0.24), residues: 1111 helix: 0.04 (0.21), residues: 581 sheet: -1.73 (0.55), residues: 82 loop : -2.54 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1564 TYR 0.017 0.001 TYR A 771 PHE 0.014 0.002 PHE A 889 TRP 0.020 0.002 TRP A1387 HIS 0.003 0.001 HIS A1524 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (11091) covalent geometry : angle 0.68453 / 0.35 (15358) hydrogen bonds : bond 0.06583 / 4.40 ( 521) hydrogen bonds : angle 5.56093 / 4.02 ( 1438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.5173 (ptt) cc_final: 0.4556 (ppp) REVERT: A 411 MET cc_start: 0.6620 (mtt) cc_final: 0.6099 (mtp) REVERT: A 746 MET cc_start: 0.9584 (tpt) cc_final: 0.9160 (tpp) REVERT: A 843 LEU cc_start: 0.9348 (mm) cc_final: 0.9109 (tp) REVERT: A 1037 LYS cc_start: 0.8926 (pttm) cc_final: 0.7590 (mppt) REVERT: A 1234 MET cc_start: 0.8816 (tpt) cc_final: 0.8461 (tpp) REVERT: A 1340 MET cc_start: 0.8959 (mmm) cc_final: 0.8513 (mmm) REVERT: A 1412 MET cc_start: 0.9422 (mmp) cc_final: 0.9101 (mmm) REVERT: A 1570 PHE cc_start: 0.5066 (t80) cc_final: 0.4709 (t80) REVERT: A 1576 LEU cc_start: 0.9635 (tt) cc_final: 0.9429 (tt) REVERT: A 1597 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8582 (mt-10) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0768 time to fit residues: 11.4721 Evaluate side-chains 74 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 4 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.059952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.046949 restraints weight = 151143.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.048018 restraints weight = 107547.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.048752 restraints weight = 83500.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049268 restraints weight = 69392.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.049660 restraints weight = 60557.092| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.169 Angle : 0.707 12.583 15358 Z= 0.362 Chirality : 0.040 0.205 1831 Planarity : 0.005 0.061 1638 Dihedral : 14.280 157.861 2210 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.54 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1111 helix: -0.01 (0.21), residues: 580 sheet: -1.73 (0.55), residues: 82 loop : -2.59 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1564 TYR 0.030 0.002 TYR A 757 PHE 0.011 0.002 PHE A1598 TRP 0.025 0.002 TRP A1387 HIS 0.004 0.001 HIS A1524 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (11091) covalent geometry : angle 0.70720 / 0.36 (15358) hydrogen bonds : bond 0.06920 / 4.61 ( 521) hydrogen bonds : angle 5.59924 / 4.05 ( 1438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.5380 (ptt) cc_final: 0.4757 (ppp) REVERT: A 393 MET cc_start: 0.9337 (tpp) cc_final: 0.9009 (tpp) REVERT: A 397 TYR cc_start: 0.8450 (m-10) cc_final: 0.8141 (m-80) REVERT: A 411 MET cc_start: 0.6696 (mtt) cc_final: 0.6207 (mtm) REVERT: A 670 PHE cc_start: 0.9471 (m-80) cc_final: 0.9132 (m-80) REVERT: A 746 MET cc_start: 0.9513 (tpt) cc_final: 0.9020 (tpt) REVERT: A 900 MET cc_start: 0.9667 (mmp) cc_final: 0.9354 (mmm) REVERT: A 1234 MET cc_start: 0.8952 (tpt) cc_final: 0.8600 (tpp) REVERT: A 1340 MET cc_start: 0.8897 (mmm) cc_final: 0.8449 (mmm) REVERT: A 1412 MET cc_start: 0.9402 (mmp) cc_final: 0.9096 (mmm) REVERT: A 1570 PHE cc_start: 0.5190 (t80) cc_final: 0.4678 (t80) REVERT: A 1576 LEU cc_start: 0.9615 (tt) cc_final: 0.9377 (tt) REVERT: A 1597 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8467 (mt-10) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0791 time to fit residues: 11.2058 Evaluate side-chains 70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.1980 chunk 86 optimal weight: 0.0020 chunk 72 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 4.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.060099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.046941 restraints weight = 152183.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048015 restraints weight = 107502.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048786 restraints weight = 83738.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.049343 restraints weight = 69414.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049722 restraints weight = 60434.284| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11091 Z= 0.163 Angle : 0.707 12.181 15358 Z= 0.360 Chirality : 0.041 0.245 1831 Planarity : 0.005 0.062 1638 Dihedral : 14.237 157.559 2210 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.72 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -1.88 (0.24), residues: 1111 helix: -0.14 (0.21), residues: 581 sheet: -1.72 (0.55), residues: 82 loop : -2.66 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1564 TYR 0.031 0.002 TYR A 757 PHE 0.017 0.002 PHE A 268 TRP 0.025 0.003 TRP A1387 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (11091) covalent geometry : angle 0.70652 / 0.36 (15358) hydrogen bonds : bond 0.06868 / 4.58 ( 521) hydrogen bonds : angle 5.57025 / 4.03 ( 1438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.5432 (ptt) cc_final: 0.4579 (ppp) REVERT: A 393 MET cc_start: 0.9261 (tpp) cc_final: 0.8974 (tpp) REVERT: A 397 TYR cc_start: 0.8377 (m-10) cc_final: 0.8122 (m-80) REVERT: A 411 MET cc_start: 0.6663 (mtt) cc_final: 0.6220 (mtm) REVERT: A 670 PHE cc_start: 0.9474 (m-80) cc_final: 0.9156 (m-80) REVERT: A 746 MET cc_start: 0.9486 (tpt) cc_final: 0.9031 (tpt) REVERT: A 900 MET cc_start: 0.9649 (mmp) cc_final: 0.9415 (mmm) REVERT: A 1037 LYS cc_start: 0.8971 (pttm) cc_final: 0.7919 (mptt) REVERT: A 1234 MET cc_start: 0.8971 (tpt) cc_final: 0.8578 (tpp) REVERT: A 1340 MET cc_start: 0.8908 (mmm) cc_final: 0.8460 (mmm) REVERT: A 1412 MET cc_start: 0.9413 (mmp) cc_final: 0.9105 (mmm) REVERT: A 1570 PHE cc_start: 0.5075 (t80) cc_final: 0.4786 (t80) REVERT: A 1576 LEU cc_start: 0.9610 (tt) cc_final: 0.9365 (tt) REVERT: A 1597 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8468 (mt-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0859 time to fit residues: 12.4405 Evaluate side-chains 69 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 24 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 119 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.060648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047605 restraints weight = 149579.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.048673 restraints weight = 106513.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049390 restraints weight = 82477.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049930 restraints weight = 68617.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050308 restraints weight = 59654.595| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11091 Z= 0.149 Angle : 0.692 12.433 15358 Z= 0.349 Chirality : 0.040 0.188 1831 Planarity : 0.005 0.063 1638 Dihedral : 14.013 157.660 2210 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1111 helix: -0.03 (0.21), residues: 577 sheet: -1.56 (0.56), residues: 82 loop : -2.57 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1564 TYR 0.029 0.002 TYR A 757 PHE 0.016 0.002 PHE A 268 TRP 0.028 0.003 TRP A1387 HIS 0.004 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (11091) covalent geometry : angle 0.69197 / 0.35 (15358) hydrogen bonds : bond 0.06832 / 4.58 ( 521) hydrogen bonds : angle 5.46209 / 3.94 ( 1438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.5562 (ptt) cc_final: 0.4626 (ppp) REVERT: A 393 MET cc_start: 0.9262 (tpp) cc_final: 0.8946 (tpp) REVERT: A 397 TYR cc_start: 0.8430 (m-10) cc_final: 0.8150 (m-80) REVERT: A 411 MET cc_start: 0.6497 (mtt) cc_final: 0.6077 (mtm) REVERT: A 670 PHE cc_start: 0.9449 (m-80) cc_final: 0.9134 (m-80) REVERT: A 746 MET cc_start: 0.9448 (tpt) cc_final: 0.8936 (tpt) REVERT: A 774 MET cc_start: 0.8495 (ttt) cc_final: 0.7272 (tpp) REVERT: A 900 MET cc_start: 0.9643 (mmp) cc_final: 0.9423 (mmm) REVERT: A 1026 MET cc_start: 0.2705 (tmm) cc_final: 0.2313 (tmm) REVERT: A 1037 LYS cc_start: 0.8907 (pttm) cc_final: 0.7523 (mptt) REVERT: A 1234 MET cc_start: 0.8954 (tpt) cc_final: 0.8547 (tpp) REVERT: A 1340 MET cc_start: 0.8896 (mmm) cc_final: 0.8444 (mmm) REVERT: A 1412 MET cc_start: 0.9456 (mmp) cc_final: 0.9140 (mmm) REVERT: A 1570 PHE cc_start: 0.5356 (t80) cc_final: 0.5015 (t80) REVERT: A 1576 LEU cc_start: 0.9593 (tt) cc_final: 0.9363 (tt) REVERT: A 1597 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8418 (mt-10) REVERT: A 1724 MET cc_start: 0.8048 (mpp) cc_final: 0.7648 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0710 time to fit residues: 10.0153 Evaluate side-chains 72 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 0.0010 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.060589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047540 restraints weight = 151717.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048578 restraints weight = 106690.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049333 restraints weight = 83054.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049852 restraints weight = 68558.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.050276 restraints weight = 59609.313| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11091 Z= 0.149 Angle : 0.694 12.022 15358 Z= 0.349 Chirality : 0.040 0.192 1831 Planarity : 0.004 0.063 1638 Dihedral : 13.912 157.983 2210 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -1.69 (0.24), residues: 1111 helix: -0.00 (0.21), residues: 580 sheet: -1.58 (0.56), residues: 82 loop : -2.54 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1564 TYR 0.028 0.002 TYR A 757 PHE 0.015 0.002 PHE A 268 TRP 0.027 0.003 TRP A1387 HIS 0.005 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (11091) covalent geometry : angle 0.69355 / 0.35 (15358) hydrogen bonds : bond 0.06909 / 4.65 ( 521) hydrogen bonds : angle 5.43317 / 3.92 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.57 seconds wall clock time: 32 minutes 30.23 seconds (1950.23 seconds total)