Starting phenix.real_space_refine on Tue Jul 29 04:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_31182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_31182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_31182.map" model { file = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_31182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ele_31182/07_2025/7ele_31182.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.90, per 1000 atoms: 0.64 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: 3.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.13 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: 5.91 Time building geometry restraints manager: 3.96 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: 6330 35.91 - 71.82: 483 71.82 - 107.73: 33 107.73 - 143.65: 1 143.65 - 179.56: 3 Dihedral angle restraints: 6850 sinusoidal: 3524 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 6847 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: 0.450 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.730 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:4.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 21.734 179.557 4690 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP A 336 HIS 0.010 0.002 HIS A 916 PHE 0.022 0.003 PHE A1392 TYR 0.021 0.003 TYR A 757 ARG 0.010 0.001 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.14768 ( 521) hydrogen bonds : angle 8.00343 ( 1438) covalent geometry : bond 0.00715 (11091) covalent geometry : angle 1.16387 (15358) *********************** 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 : 1.079 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: 0.8765 (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: 0.2825 time to fit residues: 73.8177 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 : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN A1524 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.059120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.046318 restraints weight = 152786.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047365 restraints weight = 109178.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048110 restraints weight = 85296.355| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11091 Z= 0.207 Angle : 0.791 10.152 15358 Z= 0.413 Chirality : 0.044 0.256 1831 Planarity : 0.006 0.078 1638 Dihedral : 21.068 179.552 2500 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.74 % Favored : 92.08 % Rotamer: Outliers : 0.61 % Allowed : 7.83 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.23), residues: 1111 helix: -0.92 (0.20), residues: 577 sheet: -2.72 (0.46), residues: 92 loop : -2.68 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 341 HIS 0.005 0.001 HIS A 661 PHE 0.022 0.002 PHE A1225 TYR 0.042 0.002 TYR A 757 ARG 0.014 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.07270 ( 521) hydrogen bonds : angle 6.39727 ( 1438) covalent geometry : bond 0.00413 (11091) covalent geometry : angle 0.79133 (15358) *********************** 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 101 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.006 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: A 346 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9140 (mp0) REVERT: A 381 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7914 (p-80) REVERT: A 393 MET cc_start: 0.9195 (tpt) cc_final: 0.8436 (tpp) REVERT: A 670 PHE cc_start: 0.9321 (m-80) cc_final: 0.9101 (m-80) REVERT: A 746 MET cc_start: 0.9464 (tpt) cc_final: 0.9221 (tpp) REVERT: A 763 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8476 (ttp-110) REVERT: A 774 MET cc_start: 0.8724 (ttt) cc_final: 0.6784 (tpp) REVERT: A 1340 MET cc_start: 0.9071 (mmm) cc_final: 0.8611 (mmm) REVERT: A 1412 MET cc_start: 0.9409 (mmp) cc_final: 0.9178 (mmm) REVERT: A 1758 ASN cc_start: 0.5512 (OUTLIER) cc_final: 0.5190 (m-40) outliers start: 6 outliers final: 2 residues processed: 101 average time/residue: 0.2332 time to fit residues: 33.8452 Evaluate side-chains 78 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 69 optimal weight: 0.0970 chunk 76 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** 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** ** 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** ** A1633 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.061414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.048423 restraints weight = 151840.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.049528 restraints weight = 105795.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050288 restraints weight = 81533.279| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11091 Z= 0.152 Angle : 0.698 10.624 15358 Z= 0.358 Chirality : 0.041 0.205 1831 Planarity : 0.005 0.066 1638 Dihedral : 20.561 176.862 2500 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1111 helix: -0.51 (0.20), residues: 578 sheet: -2.61 (0.47), residues: 92 loop : -2.59 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 341 HIS 0.007 0.001 HIS A 381 PHE 0.025 0.002 PHE A 556 TYR 0.030 0.002 TYR A 757 ARG 0.009 0.001 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.06425 ( 521) hydrogen bonds : angle 5.91428 ( 1438) covalent geometry : bond 0.00309 (11091) covalent geometry : angle 0.69829 (15358) *********************** 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 99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.085 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 369 MET cc_start: 0.9024 (mmp) cc_final: 0.8816 (tmm) REVERT: A 393 MET cc_start: 0.9155 (tpt) cc_final: 0.8429 (tpp) REVERT: A 411 MET cc_start: 0.7035 (mtt) cc_final: 0.6587 (mtt) REVERT: A 746 MET cc_start: 0.9507 (tpt) cc_final: 0.9108 (tpp) REVERT: A 774 MET cc_start: 0.8636 (ttt) cc_final: 0.6888 (tpp) REVERT: A 1234 MET cc_start: 0.8864 (tpt) cc_final: 0.8536 (tpp) REVERT: A 1340 MET cc_start: 0.9208 (mmm) cc_final: 0.8772 (mmm) REVERT: A 1412 MET cc_start: 0.9445 (mmp) cc_final: 0.9195 (mmm) REVERT: A 1570 PHE cc_start: 0.5376 (t80) cc_final: 0.5149 (t80) REVERT: A 1576 LEU cc_start: 0.9579 (tt) cc_final: 0.9362 (tt) REVERT: A 1724 MET cc_start: 0.7815 (mpp) cc_final: 0.7563 (mpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2238 time to fit residues: 32.3245 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 0.0020 chunk 109 optimal weight: 0.0050 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** 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** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049070 restraints weight = 148720.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.050172 restraints weight = 104394.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.050948 restraints weight = 80819.298| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3795 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= 0.140 Angle : 0.666 11.447 15358 Z= 0.338 Chirality : 0.040 0.186 1831 Planarity : 0.004 0.046 1638 Dihedral : 20.201 174.881 2500 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.28 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.24), residues: 1111 helix: -0.16 (0.21), residues: 579 sheet: -2.26 (0.49), residues: 87 loop : -2.58 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 341 HIS 0.003 0.001 HIS A1524 PHE 0.020 0.002 PHE A 556 TYR 0.022 0.001 TYR A 757 ARG 0.007 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.06410 ( 521) hydrogen bonds : angle 5.63820 ( 1438) covalent geometry : bond 0.00282 (11091) covalent geometry : angle 0.66559 (15358) *********************** 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 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.103 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: 0.9144 (tpt) cc_final: 0.8505 (tpp) REVERT: A 746 MET cc_start: 0.9610 (tpt) cc_final: 0.9142 (tpp) REVERT: A 1234 MET cc_start: 0.8935 (tpt) cc_final: 0.8730 (tpt) REVERT: A 1340 MET cc_start: 0.9095 (mmm) cc_final: 0.8591 (mmm) REVERT: A 1412 MET cc_start: 0.9482 (mmp) cc_final: 0.9198 (mmm) REVERT: A 1570 PHE cc_start: 0.5858 (t80) cc_final: 0.5514 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2309 time to fit residues: 35.8601 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 12 optimal weight: 40.0000 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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** A1523 ASN ** A1647 HIS ** 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 = 0.061069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048009 restraints weight = 149257.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.049112 restraints weight = 105630.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049898 restraints weight = 82142.386| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11091 Z= 0.150 Angle : 0.677 9.287 15358 Z= 0.345 Chirality : 0.041 0.206 1831 Planarity : 0.005 0.061 1638 Dihedral : 20.119 173.507 2500 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1111 helix: -0.14 (0.21), residues: 585 sheet: -2.31 (0.49), residues: 88 loop : -2.54 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 341 HIS 0.005 0.001 HIS A1060 PHE 0.015 0.002 PHE A1225 TYR 0.021 0.002 TYR A 757 ARG 0.014 0.001 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.06544 ( 521) hydrogen bonds : angle 5.65998 ( 1438) covalent geometry : bond 0.00301 (11091) covalent geometry : angle 0.67664 (15358) *********************** 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 100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.215 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: 0.9240 (tpt) cc_final: 0.8616 (tpp) REVERT: A 746 MET cc_start: 0.9577 (tpt) cc_final: 0.9098 (tpp) REVERT: A 1234 MET cc_start: 0.8976 (tpt) cc_final: 0.8763 (tpt) REVERT: A 1340 MET cc_start: 0.9092 (mmm) cc_final: 0.8651 (mmm) REVERT: A 1367 SER cc_start: 0.8640 (m) cc_final: 0.8399 (p) REVERT: A 1412 MET cc_start: 0.9503 (mmp) cc_final: 0.9228 (mmm) REVERT: A 1570 PHE cc_start: 0.6072 (t80) cc_final: 0.5608 (t80) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2466 time to fit residues: 36.7686 Evaluate side-chains 78 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 67 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN 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** A1420 GLN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.060401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047350 restraints weight = 149826.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.048447 restraints weight = 106665.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049196 restraints weight = 82951.574| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11091 Z= 0.163 Angle : 0.702 13.660 15358 Z= 0.355 Chirality : 0.040 0.187 1831 Planarity : 0.005 0.047 1638 Dihedral : 20.142 172.222 2500 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1111 helix: -0.13 (0.21), residues: 589 sheet: -2.33 (0.50), residues: 88 loop : -2.53 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 341 HIS 0.005 0.001 HIS A 381 PHE 0.012 0.002 PHE A 889 TYR 0.019 0.002 TYR A 757 ARG 0.008 0.001 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.06761 ( 521) hydrogen bonds : angle 5.68737 ( 1438) covalent geometry : bond 0.00330 (11091) covalent geometry : angle 0.70213 (15358) *********************** 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 100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.217 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: 0.9228 (tpt) cc_final: 0.8624 (tpp) REVERT: A 411 MET cc_start: 0.6731 (mtt) cc_final: 0.6068 (mtt) REVERT: A 670 PHE cc_start: 0.9422 (m-80) cc_final: 0.9154 (m-80) REVERT: A 746 MET cc_start: 0.9468 (tpt) cc_final: 0.8996 (tpp) REVERT: A 1234 MET cc_start: 0.8991 (tpt) cc_final: 0.8782 (tpt) REVERT: A 1340 MET cc_start: 0.8952 (mmm) cc_final: 0.8500 (mmm) REVERT: A 1367 SER cc_start: 0.8783 (m) cc_final: 0.8538 (p) REVERT: A 1412 MET cc_start: 0.9479 (mmp) cc_final: 0.9226 (mmm) REVERT: A 1570 PHE cc_start: 0.6211 (t80) cc_final: 0.5657 (t80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.2427 time to fit residues: 35.4595 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 : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 111 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 40.0000 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 overall best weight: 2.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** 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** ** A1647 HIS ** 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 = 0.3564 r_free = 0.3564 target = 0.062018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.048904 restraints weight = 149775.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.050017 restraints weight = 105917.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.050781 restraints weight = 82128.375| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4748 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= 0.135 Angle : 0.676 13.746 15358 Z= 0.341 Chirality : 0.040 0.197 1831 Planarity : 0.004 0.045 1638 Dihedral : 19.864 170.909 2500 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1111 helix: -0.06 (0.21), residues: 593 sheet: -2.08 (0.52), residues: 88 loop : -2.46 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1104 HIS 0.003 0.001 HIS A 916 PHE 0.015 0.001 PHE A 889 TYR 0.015 0.001 TYR A 757 ARG 0.008 0.001 ARG A1564 Details of bonding type rmsd hydrogen bonds : bond 0.06569 ( 521) hydrogen bonds : angle 5.57449 ( 1438) covalent geometry : bond 0.00273 (11091) covalent geometry : angle 0.67634 (15358) *********************** 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 100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.156 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: A 393 MET cc_start: 0.9229 (tpt) cc_final: 0.8781 (tpp) REVERT: A 670 PHE cc_start: 0.9360 (m-80) cc_final: 0.9120 (m-80) REVERT: A 746 MET cc_start: 0.9462 (tpt) cc_final: 0.9022 (tpp) REVERT: A 774 MET cc_start: 0.8394 (ttt) cc_final: 0.6856 (tpp) REVERT: A 843 LEU cc_start: 0.9341 (mm) cc_final: 0.9113 (tp) REVERT: A 900 MET cc_start: 0.9580 (mmp) cc_final: 0.9331 (mmm) REVERT: A 1340 MET cc_start: 0.8917 (mmm) cc_final: 0.8474 (mmm) REVERT: A 1367 SER cc_start: 0.8774 (m) cc_final: 0.8499 (p) REVERT: A 1412 MET cc_start: 0.9467 (mmp) cc_final: 0.9222 (mmm) REVERT: A 1570 PHE cc_start: 0.5920 (t80) cc_final: 0.5381 (t80) REVERT: A 1576 LEU cc_start: 0.9641 (tt) cc_final: 0.9438 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2315 time to fit residues: 33.8215 Evaluate side-chains 82 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 4 optimal weight: 0.0370 chunk 9 optimal weight: 6.9990 chunk 65 optimal weight: 0.0370 overall best weight: 2.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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** ** A1647 HIS ** 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 = 0.3576 r_free = 0.3576 target = 0.062497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049442 restraints weight = 146773.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050541 restraints weight = 103878.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.051320 restraints weight = 80217.570| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5069 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= 0.134 Angle : 0.672 13.386 15358 Z= 0.338 Chirality : 0.039 0.181 1831 Planarity : 0.004 0.043 1638 Dihedral : 19.689 169.832 2500 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1111 helix: -0.01 (0.21), residues: 595 sheet: -1.76 (0.55), residues: 82 loop : -2.47 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 341 HIS 0.003 0.001 HIS A 475 PHE 0.017 0.001 PHE A 268 TYR 0.028 0.002 TYR A 757 ARG 0.006 0.000 ARG A1564 Details of bonding type rmsd hydrogen bonds : bond 0.06719 ( 521) hydrogen bonds : angle 5.42987 ( 1438) covalent geometry : bond 0.00274 (11091) covalent geometry : angle 0.67194 (15358) *********************** 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 102 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.142 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: 0.9247 (tpt) cc_final: 0.8043 (tpp) REVERT: A 670 PHE cc_start: 0.9375 (m-80) cc_final: 0.9119 (m-80) REVERT: A 746 MET cc_start: 0.9406 (tpt) cc_final: 0.8832 (tpt) REVERT: A 900 MET cc_start: 0.9659 (mmp) cc_final: 0.9434 (mmm) REVERT: A 1234 MET cc_start: 0.9528 (mmp) cc_final: 0.9246 (tpt) REVERT: A 1340 MET cc_start: 0.8916 (mmm) cc_final: 0.8466 (mmm) REVERT: A 1367 SER cc_start: 0.8805 (m) cc_final: 0.8532 (p) REVERT: A 1412 MET cc_start: 0.9468 (mmp) cc_final: 0.9194 (mmm) REVERT: A 1724 MET cc_start: 0.7914 (mpp) cc_final: 0.7505 (mpp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2207 time to fit residues: 33.2396 Evaluate side-chains 78 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** 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** ** A1647 HIS ** 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 = 0.3580 r_free = 0.3580 target = 0.062555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049285 restraints weight = 147605.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050407 restraints weight = 103601.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.051203 restraints weight = 80146.641| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11091 Z= 0.136 Angle : 0.686 13.223 15358 Z= 0.344 Chirality : 0.040 0.226 1831 Planarity : 0.005 0.051 1638 Dihedral : 19.574 168.528 2500 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1111 helix: 0.07 (0.21), residues: 594 sheet: -1.77 (0.53), residues: 83 loop : -2.45 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 341 HIS 0.004 0.001 HIS A 984 PHE 0.020 0.002 PHE A1570 TYR 0.036 0.002 TYR A1593 ARG 0.011 0.000 ARG A1564 Details of bonding type rmsd hydrogen bonds : bond 0.06831 ( 521) hydrogen bonds : angle 5.36262 ( 1438) covalent geometry : bond 0.00278 (11091) covalent geometry : angle 0.68610 (15358) *********************** 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 98 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.217 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: A 411 MET cc_start: 0.6351 (mtt) cc_final: 0.5732 (mtt) REVERT: A 670 PHE cc_start: 0.9377 (m-80) cc_final: 0.9146 (m-80) REVERT: A 746 MET cc_start: 0.9408 (tpt) cc_final: 0.8837 (tpt) REVERT: A 1037 LYS cc_start: 0.9047 (pttm) cc_final: 0.8502 (mptt) REVERT: A 1234 MET cc_start: 0.9533 (mmp) cc_final: 0.9288 (tpt) REVERT: A 1340 MET cc_start: 0.8987 (mmm) cc_final: 0.8550 (mmm) REVERT: A 1367 SER cc_start: 0.8771 (m) cc_final: 0.8485 (p) REVERT: A 1412 MET cc_start: 0.9501 (mmp) cc_final: 0.9234 (mmm) REVERT: A 1724 MET cc_start: 0.7984 (mpp) cc_final: 0.7544 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2156 time to fit residues: 31.7280 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 : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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** A1647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.064717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051579 restraints weight = 144254.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.052686 restraints weight = 101558.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.053495 restraints weight = 78396.913| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11091 Z= 0.128 Angle : 0.676 13.244 15358 Z= 0.338 Chirality : 0.040 0.183 1831 Planarity : 0.004 0.038 1638 Dihedral : 19.237 166.070 2500 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.74 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1111 helix: 0.17 (0.21), residues: 594 sheet: -1.52 (0.57), residues: 73 loop : -2.40 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 341 HIS 0.008 0.001 HIS A 398 PHE 0.017 0.002 PHE A 889 TYR 0.036 0.002 TYR A1593 ARG 0.015 0.001 ARG A1595 Details of bonding type rmsd hydrogen bonds : bond 0.06961 ( 521) hydrogen bonds : angle 5.24780 ( 1438) covalent geometry : bond 0.00257 (11091) covalent geometry : angle 0.67555 (15358) ********************** 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 98 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.233 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: 0.9223 (m-80) cc_final: 0.9010 (m-80) REVERT: A 746 MET cc_start: 0.9422 (tpt) cc_final: 0.8817 (tpp) REVERT: A 774 MET cc_start: 0.8214 (ttt) cc_final: 0.6938 (tpt) REVERT: A 1234 MET cc_start: 0.9541 (mmp) cc_final: 0.9281 (tpt) REVERT: A 1340 MET cc_start: 0.8977 (mmm) cc_final: 0.8538 (mmm) REVERT: A 1367 SER cc_start: 0.8615 (m) cc_final: 0.8327 (p) REVERT: A 1412 MET cc_start: 0.9457 (mmp) cc_final: 0.9147 (mmm) REVERT: A 1724 MET cc_start: 0.8085 (mpp) cc_final: 0.7579 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2873 time to fit residues: 42.0939 Evaluate side-chains 79 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.062957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049678 restraints weight = 145629.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.050809 restraints weight = 103610.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051582 restraints weight = 79968.033| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11091 Z= 0.133 Angle : 0.669 12.538 15358 Z= 0.336 Chirality : 0.039 0.231 1831 Planarity : 0.004 0.036 1638 Dihedral : 19.207 163.815 2500 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.65 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.24), residues: 1111 helix: 0.20 (0.21), residues: 592 sheet: -1.67 (0.53), residues: 83 loop : -2.35 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 341 HIS 0.005 0.001 HIS A 398 PHE 0.017 0.002 PHE A 889 TYR 0.026 0.001 TYR A 757 ARG 0.008 0.000 ARG A1564 Details of bonding type rmsd hydrogen bonds : bond 0.06987 ( 521) hydrogen bonds : angle 5.25898 ( 1438) covalent geometry : bond 0.00272 (11091) covalent geometry : angle 0.66935 (15358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.77 seconds wall clock time: 65 minutes 27.19 seconds (3927.19 seconds total)