Starting phenix.real_space_refine on Wed Sep 25 18:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_31182.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_31182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_31182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_31182.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/09_2024/7ele_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-5461/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: 9.85, per 1000 atoms: 0.92 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 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: 4.00 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: 5.79 Time building geometry restraints manager: 3.10 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: 0.720 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- 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= 0.460 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 *********************** 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 fitting. rotamer outliers: 83 poor density : 122 time to evaluate : 1.176 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: 0.2693 time to fit residues: 69.7125 Evaluate side-chains 115 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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= 0.274 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.019 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: 0.9615 (tm-30) cc_final: 0.9282 (mp0) REVERT: A 381 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8256 (p-80) REVERT: A 393 MET cc_start: 0.9344 (tpt) cc_final: 0.8637 (tpp) REVERT: A 397 TYR cc_start: 0.9669 (t80) cc_final: 0.9441 (t80) REVERT: A 670 PHE cc_start: 0.9596 (m-80) cc_final: 0.9186 (m-80) REVERT: A 763 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8647 (ttp-110) REVERT: A 774 MET cc_start: 0.8896 (ttt) cc_final: 0.7612 (tpp) REVERT: A 900 MET cc_start: 0.9652 (ttp) cc_final: 0.9449 (tpp) REVERT: A 1340 MET cc_start: 0.9402 (mmm) cc_final: 0.9080 (mmm) REVERT: A 1412 MET cc_start: 0.9676 (mmp) cc_final: 0.9457 (mmm) REVERT: A 1758 ASN cc_start: 0.5232 (OUTLIER) cc_final: 0.5015 (m-40) outliers start: 6 outliers final: 2 residues processed: 101 average time/residue: 0.2335 time to fit residues: 34.0951 Evaluate side-chains 79 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 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** ** A1268 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** ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11091 Z= 0.254 Angle : 0.746 9.728 15358 Z= 0.385 Chirality : 0.042 0.197 1831 Planarity : 0.005 0.052 1638 Dihedral : 20.824 176.559 2500 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 29.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.45 % Favored : 90.37 % Rotamer: Outliers : 0.31 % Allowed : 6.41 % Favored : 93.29 % 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: -2.47 (0.23), residues: 1111 helix: -0.71 (0.20), residues: 578 sheet: -2.79 (0.45), residues: 92 loop : -2.58 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 341 HIS 0.007 0.002 HIS A 382 PHE 0.021 0.002 PHE A 556 TYR 0.029 0.002 TYR A 757 ARG 0.011 0.001 ARG A1391 *********************** 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 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.076 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: A 346 GLU cc_start: 0.9633 (tm-30) cc_final: 0.9357 (mp0) REVERT: A 369 MET cc_start: 0.9517 (mmp) cc_final: 0.9088 (tmm) REVERT: A 393 MET cc_start: 0.9310 (tpt) cc_final: 0.8603 (tpp) REVERT: A 397 TYR cc_start: 0.9682 (t80) cc_final: 0.9404 (t80) REVERT: A 411 MET cc_start: 0.7567 (mtt) cc_final: 0.7320 (mtp) REVERT: A 670 PHE cc_start: 0.9578 (m-80) cc_final: 0.9277 (m-80) REVERT: A 774 MET cc_start: 0.8544 (ttt) cc_final: 0.7583 (tpp) REVERT: A 900 MET cc_start: 0.9635 (ttp) cc_final: 0.9426 (tpp) REVERT: A 1340 MET cc_start: 0.9456 (mmm) cc_final: 0.9153 (mmm) REVERT: A 1367 SER cc_start: 0.8994 (m) cc_final: 0.8789 (p) REVERT: A 1412 MET cc_start: 0.9650 (mmp) cc_final: 0.9421 (mmm) REVERT: A 1576 LEU cc_start: 0.9697 (tt) cc_final: 0.9474 (tt) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.2184 time to fit residues: 31.3183 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** 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** A1060 HIS ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN A1776 ASN A1789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3752 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= 0.261 Angle : 0.752 10.053 15358 Z= 0.387 Chirality : 0.042 0.202 1831 Planarity : 0.005 0.057 1638 Dihedral : 20.705 174.675 2500 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % 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: -2.33 (0.24), residues: 1111 helix: -0.56 (0.20), residues: 578 sheet: -2.70 (0.46), residues: 88 loop : -2.59 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 341 HIS 0.007 0.002 HIS A1524 PHE 0.018 0.002 PHE A 556 TYR 0.023 0.002 TYR A 757 ARG 0.015 0.001 ARG A1391 *********************** 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 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.008 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 346 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9371 (mp0) REVERT: A 393 MET cc_start: 0.9337 (tpt) cc_final: 0.8682 (tpp) REVERT: A 397 TYR cc_start: 0.9693 (t80) cc_final: 0.9445 (t80) REVERT: A 411 MET cc_start: 0.7584 (mtt) cc_final: 0.7331 (mtp) REVERT: A 670 PHE cc_start: 0.9561 (m-80) cc_final: 0.9301 (m-80) REVERT: A 1339 SER cc_start: 0.9528 (t) cc_final: 0.9324 (p) REVERT: A 1340 MET cc_start: 0.9402 (mmm) cc_final: 0.8882 (mmm) REVERT: A 1367 SER cc_start: 0.9120 (m) cc_final: 0.8911 (p) REVERT: A 1412 MET cc_start: 0.9678 (mmp) cc_final: 0.9453 (mmm) REVERT: A 1576 LEU cc_start: 0.9707 (tt) cc_final: 0.9482 (tt) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1966 time to fit residues: 28.2426 Evaluate side-chains 73 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.0870 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 overall best weight: 4.0164 ------------------------------------------------------------------------------- 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 538 ASN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11091 Z= 0.207 Angle : 0.707 11.753 15358 Z= 0.359 Chirality : 0.041 0.211 1831 Planarity : 0.005 0.045 1638 Dihedral : 20.359 173.814 2500 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.72 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -2.11 (0.24), residues: 1111 helix: -0.36 (0.21), residues: 580 sheet: -2.60 (0.47), residues: 88 loop : -2.53 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1104 HIS 0.005 0.001 HIS A 382 PHE 0.017 0.002 PHE A1225 TYR 0.021 0.002 TYR A 757 ARG 0.007 0.001 ARG A1391 *********************** 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 99 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.100 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: A 346 GLU cc_start: 0.9622 (tm-30) cc_final: 0.9411 (pm20) REVERT: A 393 MET cc_start: 0.9336 (tpt) cc_final: 0.8805 (tpp) REVERT: A 397 TYR cc_start: 0.9654 (t80) cc_final: 0.9409 (t80) REVERT: A 670 PHE cc_start: 0.9497 (m-80) cc_final: 0.9225 (m-80) REVERT: A 1340 MET cc_start: 0.9378 (mmm) cc_final: 0.8972 (mmm) REVERT: A 1367 SER cc_start: 0.9144 (m) cc_final: 0.8902 (p) REVERT: A 1412 MET cc_start: 0.9688 (mmp) cc_final: 0.9470 (mmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1977 time to fit residues: 29.5461 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 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 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11091 Z= 0.237 Angle : 0.736 11.437 15358 Z= 0.373 Chirality : 0.042 0.197 1831 Planarity : 0.005 0.046 1638 Dihedral : 20.361 173.410 2500 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 31.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.99 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -2.15 (0.24), residues: 1111 helix: -0.35 (0.21), residues: 579 sheet: -2.57 (0.50), residues: 83 loop : -2.62 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 341 HIS 0.007 0.001 HIS A 326 PHE 0.013 0.002 PHE A 556 TYR 0.016 0.002 TYR A 757 ARG 0.005 0.001 ARG A1391 *********************** 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 fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.128 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 346 GLU cc_start: 0.9630 (tm-30) cc_final: 0.9421 (pm20) REVERT: A 393 MET cc_start: 0.9344 (tpt) cc_final: 0.8821 (tpp) REVERT: A 397 TYR cc_start: 0.9670 (t80) cc_final: 0.9434 (t80) REVERT: A 411 MET cc_start: 0.7522 (mtt) cc_final: 0.7199 (mtt) REVERT: A 670 PHE cc_start: 0.9485 (m-80) cc_final: 0.9217 (m-80) REVERT: A 746 MET cc_start: 0.9001 (tpt) cc_final: 0.8754 (tpt) REVERT: A 1340 MET cc_start: 0.9270 (mmm) cc_final: 0.8919 (mmm) REVERT: A 1367 SER cc_start: 0.9204 (m) cc_final: 0.8998 (p) REVERT: A 1412 MET cc_start: 0.9695 (mmp) cc_final: 0.9472 (mmm) REVERT: A 1576 LEU cc_start: 0.9684 (tt) cc_final: 0.9465 (tt) REVERT: A 1597 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7905 (mt-10) REVERT: A 1724 MET cc_start: 0.7736 (mpp) cc_final: 0.7473 (mpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2076 time to fit residues: 30.1475 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 85 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11091 Z= 0.187 Angle : 0.698 14.619 15358 Z= 0.349 Chirality : 0.040 0.176 1831 Planarity : 0.005 0.053 1638 Dihedral : 20.075 173.562 2500 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % 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: -1.96 (0.24), residues: 1111 helix: -0.15 (0.21), residues: 580 sheet: -2.42 (0.51), residues: 83 loop : -2.62 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1104 HIS 0.004 0.001 HIS A 326 PHE 0.015 0.002 PHE A 889 TYR 0.029 0.002 TYR A 757 ARG 0.004 0.000 ARG A 295 *********************** 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 fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9606 (tm-30) cc_final: 0.9377 (pm20) REVERT: A 369 MET cc_start: 0.9028 (mtp) cc_final: 0.8163 (ttp) REVERT: A 393 MET cc_start: 0.9424 (tpt) cc_final: 0.9122 (tpp) REVERT: A 397 TYR cc_start: 0.9660 (t80) cc_final: 0.9417 (t80) REVERT: A 411 MET cc_start: 0.7316 (mtt) cc_final: 0.6990 (mtt) REVERT: A 670 PHE cc_start: 0.9373 (m-80) cc_final: 0.9011 (m-80) REVERT: A 746 MET cc_start: 0.9002 (tpt) cc_final: 0.8665 (tpp) REVERT: A 774 MET cc_start: 0.8053 (ttt) cc_final: 0.7439 (tpp) REVERT: A 982 LEU cc_start: 0.9469 (pp) cc_final: 0.9209 (pp) REVERT: A 1026 MET cc_start: 0.2523 (tmm) cc_final: 0.2254 (tmm) REVERT: A 1037 LYS cc_start: 0.9109 (pttm) cc_final: 0.7933 (mppt) REVERT: A 1340 MET cc_start: 0.9239 (mmm) cc_final: 0.8893 (mmm) REVERT: A 1367 SER cc_start: 0.9182 (m) cc_final: 0.8940 (p) REVERT: A 1412 MET cc_start: 0.9695 (mmp) cc_final: 0.9477 (mmm) REVERT: A 1724 MET cc_start: 0.7761 (mpp) cc_final: 0.7539 (mpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1909 time to fit residues: 28.3337 Evaluate side-chains 72 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 111 optimal weight: 30.0000 chunk 101 optimal weight: 40.0000 chunk 108 optimal weight: 0.9980 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 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 424 GLN ** 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** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11091 Z= 0.192 Angle : 0.692 14.006 15358 Z= 0.348 Chirality : 0.040 0.178 1831 Planarity : 0.004 0.045 1638 Dihedral : 19.920 174.311 2500 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % 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: -1.89 (0.24), residues: 1111 helix: -0.11 (0.21), residues: 583 sheet: -2.22 (0.51), residues: 83 loop : -2.61 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 341 HIS 0.004 0.001 HIS A 326 PHE 0.028 0.002 PHE A 396 TYR 0.031 0.001 TYR A 757 ARG 0.003 0.000 ARG A 740 *********************** 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 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.170 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 297 MET cc_start: 0.8807 (mtt) cc_final: 0.8508 (mmm) REVERT: A 369 MET cc_start: 0.9081 (mtp) cc_final: 0.8232 (ttp) REVERT: A 393 MET cc_start: 0.9353 (tpt) cc_final: 0.8870 (tpp) REVERT: A 397 TYR cc_start: 0.9655 (t80) cc_final: 0.9412 (t80) REVERT: A 670 PHE cc_start: 0.9413 (m-80) cc_final: 0.9135 (m-10) REVERT: A 982 LEU cc_start: 0.9465 (pp) cc_final: 0.9223 (pp) REVERT: A 1037 LYS cc_start: 0.9072 (pttm) cc_final: 0.7918 (mppt) REVERT: A 1340 MET cc_start: 0.9230 (mmm) cc_final: 0.8882 (mmm) REVERT: A 1367 SER cc_start: 0.9208 (m) cc_final: 0.8976 (p) REVERT: A 1412 MET cc_start: 0.9702 (mmp) cc_final: 0.9474 (mmm) REVERT: A 1576 LEU cc_start: 0.9666 (tt) cc_final: 0.9460 (tt) REVERT: A 1597 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7931 (mt-10) REVERT: A 1724 MET cc_start: 0.7764 (mpp) cc_final: 0.7322 (mpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1940 time to fit residues: 28.4233 Evaluate side-chains 73 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS 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** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11091 Z= 0.193 Angle : 0.697 13.318 15358 Z= 0.349 Chirality : 0.040 0.224 1831 Planarity : 0.004 0.040 1638 Dihedral : 19.794 175.603 2500 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.45 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -1.78 (0.24), residues: 1111 helix: -0.04 (0.21), residues: 586 sheet: -2.10 (0.52), residues: 83 loop : -2.57 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 341 HIS 0.004 0.001 HIS A 326 PHE 0.018 0.002 PHE A 396 TYR 0.029 0.001 TYR A 757 ARG 0.003 0.000 ARG A 295 *********************** 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 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8716 (mtt) cc_final: 0.8400 (mmm) REVERT: A 346 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9345 (pm20) REVERT: A 369 MET cc_start: 0.9070 (mtp) cc_final: 0.8252 (ttp) REVERT: A 393 MET cc_start: 0.9391 (tpt) cc_final: 0.8945 (tpp) REVERT: A 397 TYR cc_start: 0.9652 (t80) cc_final: 0.9391 (t80) REVERT: A 411 MET cc_start: 0.6902 (mtt) cc_final: 0.6682 (mtt) REVERT: A 670 PHE cc_start: 0.9439 (m-80) cc_final: 0.9160 (m-10) REVERT: A 774 MET cc_start: 0.8017 (ttt) cc_final: 0.7553 (tpp) REVERT: A 1340 MET cc_start: 0.9226 (mmm) cc_final: 0.8881 (mmm) REVERT: A 1412 MET cc_start: 0.9705 (mmp) cc_final: 0.9478 (mmm) REVERT: A 1724 MET cc_start: 0.7778 (mpp) cc_final: 0.7331 (mpp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1933 time to fit residues: 28.1628 Evaluate side-chains 70 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11091 Z= 0.272 Angle : 0.779 12.523 15358 Z= 0.398 Chirality : 0.042 0.224 1831 Planarity : 0.005 0.043 1638 Dihedral : 20.075 177.528 2500 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 34.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.26 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -2.13 (0.24), residues: 1111 helix: -0.46 (0.20), residues: 590 sheet: -2.39 (0.51), residues: 83 loop : -2.48 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 547 HIS 0.008 0.002 HIS A 808 PHE 0.018 0.002 PHE A 301 TYR 0.030 0.002 TYR A 757 ARG 0.006 0.001 ARG A1736 ********************** 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 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.112 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 346 GLU cc_start: 0.9569 (tm-30) cc_final: 0.9321 (pm20) REVERT: A 369 MET cc_start: 0.9236 (mtp) cc_final: 0.8319 (ttp) REVERT: A 393 MET cc_start: 0.9405 (tpt) cc_final: 0.8923 (tpp) REVERT: A 397 TYR cc_start: 0.9669 (t80) cc_final: 0.9433 (t80) REVERT: A 411 MET cc_start: 0.7216 (mtt) cc_final: 0.6914 (mtt) REVERT: A 670 PHE cc_start: 0.9497 (m-80) cc_final: 0.9249 (m-10) REVERT: A 1340 MET cc_start: 0.9230 (mmm) cc_final: 0.8872 (mmm) REVERT: A 1412 MET cc_start: 0.9717 (mmp) cc_final: 0.9486 (mmm) REVERT: A 1576 LEU cc_start: 0.9635 (tt) cc_final: 0.9420 (tt) REVERT: A 1597 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7935 (mt-10) REVERT: A 1724 MET cc_start: 0.7930 (mpp) cc_final: 0.7518 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1951 time to fit residues: 28.0724 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 433 ASN ** 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** ** 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 = 0.3571 r_free = 0.3571 target = 0.062216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049016 restraints weight = 147690.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050132 restraints weight = 104787.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.050903 restraints weight = 80984.982| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5564 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= 0.182 Angle : 0.701 13.377 15358 Z= 0.349 Chirality : 0.040 0.178 1831 Planarity : 0.005 0.040 1638 Dihedral : 19.618 179.991 2500 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.75 (0.24), residues: 1111 helix: -0.13 (0.21), residues: 598 sheet: -1.91 (0.55), residues: 73 loop : -2.47 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 341 HIS 0.008 0.001 HIS A 381 PHE 0.018 0.001 PHE A 396 TYR 0.030 0.001 TYR A 757 ARG 0.004 0.000 ARG A1335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.18 seconds wall clock time: 34 minutes 54.54 seconds (2094.54 seconds total)