Starting phenix.real_space_refine on Fri Sep 11 18:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ele_31182/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.map" model { file = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_2026/7ele_31182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ele_31182/09_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-2.2.1-6174/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: {'RNAv2': 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: 0.91 Conformation dependent library (CDL) restraints added in 462.5 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: 1.36 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: 2.86 Time building geometry restraints manager: 1.21 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: 13969 2.04 - 4.07: 1227 4.07 - 6.11: 125 6.11 - 8.14: 30 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=" 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 angle pdb=" CA ILE A 366 " pdb=" C ILE A 366 " pdb=" O ILE A 366 " ideal model delta sigma weight residual 121.59 116.53 5.06 1.03e+00 9.43e-01 2.42e+01 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 6085 34.39 - 68.78: 459 68.78 - 103.17: 14 103.17 - 137.57: 0 137.57 - 171.96: 2 Dihedral angle restraints: 6560 sinusoidal: 3234 harmonic: 3326 Sorted by residual: dihedral pdb=" C4' C G 89 " pdb=" C3' C G 89 " pdb=" C2' C G 89 " pdb=" C1' C G 89 " ideal model delta sinusoidal sigma weight residual 36.34 -33.77 70.12 1 3.10e+00 1.04e-01 6.59e+02 dihedral pdb=" C4' U G 81 " pdb=" C3' U G 81 " pdb=" C2' U G 81 " pdb=" C1' U G 81 " ideal model delta sinusoidal sigma weight residual 36.34 -33.36 69.71 1 3.10e+00 1.04e-01 6.52e+02 dihedral pdb=" O4' U G 81 " pdb=" C4' U G 81 " pdb=" C3' U G 81 " pdb=" C2' U G 81 " ideal model delta sinusoidal sigma weight residual -35.15 25.66 -60.81 1 4.00e+00 6.25e-02 3.07e+02 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1469 0.091 - 0.182: 243 0.182 - 0.272: 111 0.272 - 0.363: 7 0.363 - 0.454: 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 -2.50 -2.04 -0.45 2.00e-01 2.50e+01 5.15e+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 -2.79 -2.43 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" P A G 3 " pdb=" OP1 A G 3 " pdb=" OP2 A G 3 " pdb=" O5' A G 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.35 2.00e-01 2.50e+01 3.13e+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: 0.680 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: 13.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- 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= 0.456 Angle : 1.207 10.177 15358 Z= 0.712 Chirality : 0.082 0.454 1831 Planarity : 0.006 0.063 1638 Dihedral : 20.092 171.957 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 0.00718 / 0.46 (11091) covalent geometry : angle 1.20715 / 0.71 (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 : 0.381 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: 0.1190 time to fit residues: 31.3295 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 : 0.370 ------------------------------------------------------------------------------- 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: 9.9990 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** ** 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** A1758 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.061498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048548 restraints weight = 151250.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049676 restraints weight = 105440.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050476 restraints weight = 81471.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.051058 restraints weight = 67551.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051423 restraints weight = 58418.166| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11091 Z= 0.176 Angle : 0.895 16.030 15358 Z= 0.415 Chirality : 0.055 0.509 1831 Planarity : 0.005 0.075 1638 Dihedral : 15.333 177.451 2210 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.47 % Favored : 92.35 % Rotamer: Outliers : 0.61 % Allowed : 6.71 % Favored : 92.68 % 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: -2.49 (0.23), residues: 1111 helix: -0.79 (0.20), residues: 576 sheet: -2.65 (0.44), residues: 104 loop : -2.50 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1391 TYR 0.036 0.002 TYR A 757 PHE 0.019 0.002 PHE A1225 TRP 0.042 0.003 TRP A 341 HIS 0.004 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (11091) covalent geometry : angle 0.89516 / 0.42 (15358) hydrogen bonds : bond 0.06812 / 4.54 ( 521) hydrogen bonds : angle 6.24558 / 4.52 ( 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 : 0.388 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: 0.9405 (tm-30) cc_final: 0.9113 (mp0) REVERT: A 393 MET cc_start: 0.9172 (tpt) cc_final: 0.8390 (tpp) REVERT: A 411 MET cc_start: 0.6982 (mtt) cc_final: 0.6618 (mtt) REVERT: A 746 MET cc_start: 0.9452 (tpt) cc_final: 0.9235 (tpp) REVERT: A 774 MET cc_start: 0.8660 (ttt) cc_final: 0.6614 (tpp) REVERT: A 1234 MET cc_start: 0.8870 (tpt) cc_final: 0.8663 (tpt) REVERT: A 1340 MET cc_start: 0.9038 (mmm) cc_final: 0.8585 (mmm) REVERT: A 1570 PHE cc_start: 0.5090 (t80) cc_final: 0.4618 (t80) REVERT: A 1576 LEU cc_start: 0.9569 (tt) cc_final: 0.9359 (tt) REVERT: A 1646 LEU cc_start: 0.9163 (mm) cc_final: 0.8619 (mm) outliers start: 6 outliers final: 1 residues processed: 114 average time/residue: 0.0976 time to fit residues: 16.3828 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 : 0.305 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A1428 GLN A1647 HIS A1758 ASN A1776 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.048528 restraints weight = 150466.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.049640 restraints weight = 105081.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.050424 restraints weight = 81382.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050990 restraints weight = 67710.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051369 restraints weight = 58869.384| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11091 Z= 0.157 Angle : 0.825 14.868 15358 Z= 0.380 Chirality : 0.054 0.675 1831 Planarity : 0.005 0.064 1638 Dihedral : 14.641 174.897 2210 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.19 % Favored : 91.63 % Rotamer: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % 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: -2.13 (0.24), residues: 1111 helix: -0.37 (0.21), residues: 581 sheet: -2.23 (0.51), residues: 87 loop : -2.64 (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 0.030 0.002 PHE A 556 TRP 0.023 0.003 TRP A 341 HIS 0.003 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (11091) covalent geometry : angle 0.82522 / 0.38 (15358) hydrogen bonds : bond 0.06404 / 4.28 ( 521) hydrogen bonds : angle 5.84995 / 4.24 ( 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 104 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.338 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 393 MET cc_start: 0.9175 (tpt) cc_final: 0.8519 (tpp) REVERT: A 746 MET cc_start: 0.9565 (tpt) cc_final: 0.8525 (mmm) REVERT: A 774 MET cc_start: 0.8559 (ttt) cc_final: 0.6780 (tpp) REVERT: A 1234 MET cc_start: 0.8873 (tpt) cc_final: 0.8665 (tpt) REVERT: A 1340 MET cc_start: 0.9167 (mmm) cc_final: 0.8724 (mmm) REVERT: A 1412 MET cc_start: 0.9398 (mmp) cc_final: 0.9113 (mmm) REVERT: A 1576 LEU cc_start: 0.9568 (tt) cc_final: 0.9342 (tt) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1047 time to fit residues: 15.6523 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 : 0.358 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 30 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 overall best weight: 2.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** 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** ** A1523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN A1758 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.063296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050280 restraints weight = 148455.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051432 restraints weight = 103346.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052210 restraints weight = 79288.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.052767 restraints weight = 65487.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.053176 restraints weight = 56830.100| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11091 Z= 0.139 Angle : 0.782 13.657 15358 Z= 0.356 Chirality : 0.051 0.567 1831 Planarity : 0.004 0.047 1638 Dihedral : 14.292 172.666 2210 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.74 % Favored : 92.08 % Rotamer: Outliers : 0.20 % Allowed : 4.48 % 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: -1.82 (0.24), residues: 1111 helix: -0.12 (0.21), residues: 583 sheet: -1.84 (0.53), residues: 87 loop : -2.57 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1391 TYR 0.025 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 0.00282 / 0.14 (11091) covalent geometry : angle 0.78159 / 0.36 (15358) hydrogen bonds : bond 0.06265 / 4.21 ( 521) hydrogen bonds : angle 5.55160 / 4.05 ( 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 114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.386 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: A 393 MET cc_start: 0.9212 (tpt) cc_final: 0.8564 (tpp) REVERT: A 746 MET cc_start: 0.9611 (tpt) cc_final: 0.8571 (mmm) REVERT: A 1340 MET cc_start: 0.9188 (mmm) cc_final: 0.8720 (mmm) REVERT: A 1412 MET cc_start: 0.9459 (mmp) cc_final: 0.9148 (mmm) REVERT: A 1646 LEU cc_start: 0.9175 (mm) cc_final: 0.8657 (mm) REVERT: A 1758 ASN cc_start: 0.5140 (OUTLIER) cc_final: 0.4707 (m-40) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.1040 time to fit residues: 17.1352 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 : 0.630 ------------------------------------------------------------------------------- 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: 20.0000 chunk 103 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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** ** A1636 ASN ** 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 = 0.3505 r_free = 0.3505 target = 0.058991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.045841 restraints weight = 152034.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.046869 restraints weight = 109319.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047590 restraints weight = 86271.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.048083 restraints weight = 72470.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048487 restraints weight = 63919.036| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11091 Z= 0.206 Angle : 0.857 12.798 15358 Z= 0.398 Chirality : 0.053 0.593 1831 Planarity : 0.005 0.053 1638 Dihedral : 14.291 171.758 2210 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 30.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -1.96 (0.24), residues: 1111 helix: -0.26 (0.20), residues: 582 sheet: -2.17 (0.51), residues: 82 loop : -2.52 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1391 TYR 0.021 0.002 TYR A 757 PHE 0.014 0.002 PHE A1392 TRP 0.013 0.002 TRP A1528 HIS 0.007 0.002 HIS A1401 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (11091) covalent geometry : angle 0.85663 / 0.40 (15358) hydrogen bonds : bond 0.07285 / 4.91 ( 521) hydrogen bonds : angle 5.87234 / 4.27 ( 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 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.409 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: A 393 MET cc_start: 0.9176 (tpt) cc_final: 0.8579 (tpp) REVERT: A 411 MET cc_start: 0.6706 (mtt) cc_final: 0.6067 (mtt) REVERT: A 746 MET cc_start: 0.9534 (tpt) cc_final: 0.9041 (tpp) REVERT: A 1234 MET cc_start: 0.8828 (tpt) cc_final: 0.8594 (tpt) REVERT: A 1340 MET cc_start: 0.9002 (mmm) cc_final: 0.8562 (mmm) REVERT: A 1367 SER cc_start: 0.8719 (m) cc_final: 0.8503 (p) REVERT: A 1412 MET cc_start: 0.9495 (mmp) cc_final: 0.9184 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1013 time to fit residues: 13.5060 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 : 0.352 ------------------------------------------------------------------------------- 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: 40.0000 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN A 660 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** ** A1633 ASN ** 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 = 0.3531 r_free = 0.3531 target = 0.060284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047123 restraints weight = 150217.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048190 restraints weight = 107060.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.048934 restraints weight = 84087.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049473 restraints weight = 70317.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.049895 restraints weight = 61191.901| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4562 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= 0.167 Angle : 0.815 13.308 15358 Z= 0.375 Chirality : 0.052 0.543 1831 Planarity : 0.005 0.047 1638 Dihedral : 14.259 172.261 2210 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -1.91 (0.24), residues: 1111 helix: -0.15 (0.21), residues: 582 sheet: -2.30 (0.49), residues: 88 loop : -2.55 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1391 TYR 0.022 0.002 TYR A 757 PHE 0.013 0.002 PHE A 889 TRP 0.015 0.002 TRP A1104 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (11091) covalent geometry : angle 0.81509 / 0.37 (15358) hydrogen bonds : bond 0.06826 / 4.65 ( 521) hydrogen bonds : angle 5.73369 / 4.15 ( 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 97 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.470 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 670 PHE cc_start: 0.9425 (m-80) cc_final: 0.9149 (m-80) REVERT: A 746 MET cc_start: 0.9466 (tpt) cc_final: 0.9030 (tpp) REVERT: A 1037 LYS cc_start: 0.8958 (pttm) cc_final: 0.7770 (mptt) REVERT: A 1234 MET cc_start: 0.8909 (tpt) cc_final: 0.8510 (tpp) REVERT: A 1340 MET cc_start: 0.8964 (mmm) cc_final: 0.8510 (mmm) REVERT: A 1367 SER cc_start: 0.8741 (m) cc_final: 0.8474 (p) REVERT: A 1412 MET cc_start: 0.9454 (mmp) cc_final: 0.9152 (mmm) REVERT: A 1657 LEU cc_start: 0.9438 (tp) cc_final: 0.9184 (pp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1064 time to fit residues: 15.0412 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 : 0.462 ------------------------------------------------------------------------------- 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: 20.0000 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.061238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048033 restraints weight = 148677.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.049120 restraints weight = 105742.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049887 restraints weight = 82589.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.050447 restraints weight = 68810.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.050822 restraints weight = 59901.358| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4913 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= 0.144 Angle : 0.782 13.499 15358 Z= 0.359 Chirality : 0.051 0.502 1831 Planarity : 0.004 0.045 1638 Dihedral : 14.078 171.674 2210 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -1.78 (0.24), residues: 1111 helix: -0.07 (0.21), residues: 585 sheet: -1.92 (0.54), residues: 82 loop : -2.57 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1564 TYR 0.018 0.002 TYR A 757 PHE 0.014 0.001 PHE A 889 TRP 0.012 0.002 TRP A 547 HIS 0.008 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (11091) covalent geometry : angle 0.78245 / 0.36 (15358) hydrogen bonds : bond 0.06685 / 4.59 ( 521) hydrogen bonds : angle 5.55767 / 4.04 ( 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 97 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.367 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 411 MET cc_start: 0.6712 (mtt) cc_final: 0.6174 (mtt) REVERT: A 670 PHE cc_start: 0.9389 (m-80) cc_final: 0.9123 (m-80) REVERT: A 746 MET cc_start: 0.9453 (tpt) cc_final: 0.9032 (tpp) REVERT: A 774 MET cc_start: 0.8461 (ttt) cc_final: 0.7010 (tpp) REVERT: A 890 GLU cc_start: 0.8108 (mp0) cc_final: 0.7559 (mp0) REVERT: A 900 MET cc_start: 0.9535 (mmp) cc_final: 0.9276 (mmm) REVERT: A 1037 LYS cc_start: 0.8940 (pttm) cc_final: 0.7664 (mppt) REVERT: A 1234 MET cc_start: 0.8923 (tpt) cc_final: 0.8518 (tpp) REVERT: A 1340 MET cc_start: 0.8876 (mmm) cc_final: 0.8412 (mmm) REVERT: A 1367 SER cc_start: 0.8778 (m) cc_final: 0.8487 (p) REVERT: A 1412 MET cc_start: 0.9483 (mmp) cc_final: 0.9151 (mmm) REVERT: A 1597 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8771 (tt0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1034 time to fit residues: 14.5195 Evaluate side-chains 77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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 = 0.3591 r_free = 0.3591 target = 0.062926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049823 restraints weight = 145916.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050945 restraints weight = 102615.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051720 restraints weight = 79230.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052263 restraints weight = 65518.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.052676 restraints weight = 57060.981| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5321 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= 0.135 Angle : 0.777 13.404 15358 Z= 0.359 Chirality : 0.051 0.457 1831 Planarity : 0.004 0.045 1638 Dihedral : 13.775 171.173 2210 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.72 % 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: -1.63 (0.24), residues: 1111 helix: -0.02 (0.21), residues: 592 sheet: -1.69 (0.60), residues: 68 loop : -2.44 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1564 TYR 0.028 0.001 TYR A 757 PHE 0.016 0.001 PHE A 889 TRP 0.013 0.002 TRP A1104 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (11091) covalent geometry : angle 0.77742 / 0.36 (15358) hydrogen bonds : bond 0.06760 / 4.67 ( 521) hydrogen bonds : angle 5.40213 / 3.94 ( 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 100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.370 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 411 MET cc_start: 0.6453 (mtt) cc_final: 0.5950 (mtm) REVERT: A 670 PHE cc_start: 0.9338 (m-80) cc_final: 0.8991 (m-80) REVERT: A 746 MET cc_start: 0.9392 (tpt) cc_final: 0.8711 (tpt) REVERT: A 900 MET cc_start: 0.9591 (mmp) cc_final: 0.9367 (mmm) REVERT: A 1037 LYS cc_start: 0.8800 (pttm) cc_final: 0.7511 (mppt) REVERT: A 1234 MET cc_start: 0.8961 (tpt) cc_final: 0.8528 (tpp) REVERT: A 1340 MET cc_start: 0.8841 (mmm) cc_final: 0.8374 (mmm) REVERT: A 1367 SER cc_start: 0.8767 (m) cc_final: 0.8485 (p) REVERT: A 1412 MET cc_start: 0.9484 (mmp) cc_final: 0.9152 (mmm) REVERT: A 1570 PHE cc_start: 0.5222 (t80) cc_final: 0.4734 (t80) REVERT: A 1576 LEU cc_start: 0.9648 (tp) cc_final: 0.9385 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0958 time to fit residues: 14.3213 Evaluate side-chains 77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 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 = 0.059898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.046655 restraints weight = 150503.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047694 restraints weight = 107259.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048443 restraints weight = 84216.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048973 restraints weight = 70300.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.049381 restraints weight = 61358.404| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11091 Z= 0.181 Angle : 0.829 12.731 15358 Z= 0.389 Chirality : 0.051 0.476 1831 Planarity : 0.005 0.044 1638 Dihedral : 13.802 170.692 2210 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.36 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.82 (0.24), residues: 1111 helix: -0.14 (0.21), residues: 590 sheet: -1.87 (0.52), residues: 83 loop : -2.57 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1564 TYR 0.029 0.002 TYR A 757 PHE 0.025 0.002 PHE A1637 TRP 0.012 0.002 TRP A 547 HIS 0.005 0.001 HIS A1401 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (11091) covalent geometry : angle 0.82905 / 0.39 (15358) hydrogen bonds : bond 0.07132 / 4.88 ( 521) hydrogen bonds : angle 5.65556 / 4.11 ( 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 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.365 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 411 MET cc_start: 0.6746 (mtt) cc_final: 0.6182 (mtt) REVERT: A 670 PHE cc_start: 0.9423 (m-80) cc_final: 0.9020 (m-10) REVERT: A 746 MET cc_start: 0.9372 (tpt) cc_final: 0.8894 (tpt) REVERT: A 1037 LYS cc_start: 0.9004 (pttm) cc_final: 0.7925 (mptt) REVERT: A 1234 MET cc_start: 0.9020 (tpt) cc_final: 0.8764 (tpt) REVERT: A 1340 MET cc_start: 0.8880 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1367 SER cc_start: 0.8848 (m) cc_final: 0.8561 (p) REVERT: A 1412 MET cc_start: 0.9460 (mmp) cc_final: 0.9137 (mmm) REVERT: A 1570 PHE cc_start: 0.5467 (t80) cc_final: 0.4951 (t80) REVERT: A 1576 LEU cc_start: 0.9664 (tp) cc_final: 0.9382 (tt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0908 time to fit residues: 12.6542 Evaluate side-chains 71 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 10.0000 chunk 79 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 111 optimal weight: 40.0000 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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** A1523 ASN A1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.045468 restraints weight = 150328.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.046487 restraints weight = 107362.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.047216 restraints weight = 84030.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.047734 restraints weight = 70083.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048124 restraints weight = 61316.020| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11091 Z= 0.198 Angle : 0.862 12.156 15358 Z= 0.406 Chirality : 0.053 0.492 1831 Planarity : 0.005 0.053 1638 Dihedral : 13.956 171.873 2210 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 30.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.44 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -2.21 (0.23), residues: 1111 helix: -0.51 (0.20), residues: 594 sheet: -2.18 (0.51), residues: 83 loop : -2.63 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1564 TYR 0.031 0.002 TYR A 757 PHE 0.016 0.002 PHE A 889 TRP 0.013 0.002 TRP A1104 HIS 0.006 0.002 HIS A1401 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (11091) covalent geometry : angle 0.86198 / 0.41 (15358) hydrogen bonds : bond 0.07319 / 5.01 ( 521) hydrogen bonds : angle 5.87553 / 4.25 ( 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 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.385 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 393 MET cc_start: 0.9764 (mmp) cc_final: 0.9496 (tpp) REVERT: A 411 MET cc_start: 0.6954 (mtt) cc_final: 0.6350 (mtt) REVERT: A 670 PHE cc_start: 0.9415 (m-80) cc_final: 0.8970 (m-10) REVERT: A 746 MET cc_start: 0.9306 (tpt) cc_final: 0.8803 (tpt) REVERT: A 1234 MET cc_start: 0.9047 (tpt) cc_final: 0.8769 (tpt) REVERT: A 1340 MET cc_start: 0.8856 (mmm) cc_final: 0.8413 (mmm) REVERT: A 1412 MET cc_start: 0.9536 (mmp) cc_final: 0.9191 (mmm) REVERT: A 1570 PHE cc_start: 0.5638 (t80) cc_final: 0.4985 (t80) REVERT: A 1576 LEU cc_start: 0.9654 (tp) cc_final: 0.9375 (tp) REVERT: A 1724 MET cc_start: 0.8059 (mpp) cc_final: 0.7676 (mpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0918 time to fit residues: 12.3976 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 : 0.271 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.060782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047558 restraints weight = 149403.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048686 restraints weight = 105694.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.049464 restraints weight = 81648.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049998 restraints weight = 67351.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050418 restraints weight = 58605.769| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11091 Z= 0.148 Angle : 0.797 12.060 15358 Z= 0.370 Chirality : 0.051 0.461 1831 Planarity : 0.004 0.041 1638 Dihedral : 13.784 171.736 2210 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.64 % Favored : 91.18 % 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: -1.99 (0.24), residues: 1111 helix: -0.30 (0.20), residues: 595 sheet: -1.96 (0.51), residues: 83 loop : -2.61 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1564 TYR 0.029 0.002 TYR A 757 PHE 0.017 0.001 PHE A 889 TRP 0.015 0.002 TRP A 547 HIS 0.005 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (11091) covalent geometry : angle 0.79750 / 0.37 (15358) hydrogen bonds : bond 0.06779 / 4.70 ( 521) hydrogen bonds : angle 5.60260 / 4.05 ( 1438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.97 seconds wall clock time: 35 minutes 38.93 seconds (2138.93 seconds total)