Starting phenix.real_space_refine on Fri Jul 3 06:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.map" model { file = "/net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cb_67570/07_2026/21cb_67570.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.051 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 58 5.49 5 S 60 5.16 5 C 7518 2.51 5 N 2077 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12141 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 10903 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 80, 'TRANS': 1276} Chain breaks: 6 Chain: "B" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1238 Classifications: {'RNA': 58} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 56} Chain breaks: 1 Time building chain proxies: 2.21, per 1000 atoms: 0.18 Number of scatterers: 12141 At special positions: 0 Unit cell: (93.539, 99.845, 160.803, 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 58 15.00 O 2428 8.00 N 2077 7.00 C 7518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 531 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 375.1 milliseconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2602 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 50.2% alpha, 5.9% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.378A pdb=" N GLU A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 69 through 81 Processing helix chain 'A' and resid 81 through 86 removed outlier: 4.091A pdb=" N ILE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 86' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 176 through 182 removed outlier: 4.353A pdb=" N LEU A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.663A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.897A pdb=" N ILE A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 339 through 363 removed outlier: 3.943A pdb=" N PHE A 363 " --> pdb=" O CYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 451 through 466 removed outlier: 4.065A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 removed outlier: 4.418A pdb=" N TYR A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 568 through 589 removed outlier: 3.618A pdb=" N LYS A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 641 removed outlier: 3.585A pdb=" N THR A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 705 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.755A pdb=" N MET A 713 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.650A pdb=" N THR A 798 " --> pdb=" O PRO A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 894 through 903 Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.735A pdb=" N TYR A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 977 Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'A' and resid 1044 through 1076 removed outlier: 3.900A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1054 " --> pdb=" O LYS A1050 " (cutoff:3.500A) Proline residue: A1055 - end of helix removed outlier: 3.689A pdb=" N THR A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1312 through 1335 removed outlier: 3.653A pdb=" N LEU A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.896A pdb=" N LYS A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 3.607A pdb=" N ARG A1368 " --> pdb=" O GLY A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1557 through 1587 removed outlier: 8.155A pdb=" N GLU A1576 " --> pdb=" O THR A1572 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ARG A1577 " --> pdb=" O SER A1573 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A1578 " --> pdb=" O CYS A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1674 removed outlier: 4.326A pdb=" N LEU A1659 " --> pdb=" O ALA A1655 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LYS A1671 " --> pdb=" O GLU A1667 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS A1672 " --> pdb=" O ASN A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1687 removed outlier: 4.195A pdb=" N LEU A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1723 removed outlier: 4.065A pdb=" N ALA A1710 " --> pdb=" O PHE A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1740 Processing helix chain 'A' and resid 1741 through 1752 Processing helix chain 'A' and resid 1754 through 1758 Processing helix chain 'A' and resid 1762 through 1779 Processing helix chain 'A' and resid 1805 through 1823 removed outlier: 3.912A pdb=" N GLY A1809 " --> pdb=" O PRO A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1848 Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix removed outlier: 3.603A pdb=" N ASN A1848 " --> pdb=" O LYS A1844 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1912 removed outlier: 3.941A pdb=" N ARG A1907 " --> pdb=" O ALA A1903 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A1908 " --> pdb=" O ALA A1904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.788A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 517 removed outlier: 6.757A pdb=" N GLY A 444 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 535 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 654 through 657 removed outlier: 3.729A pdb=" N ARG A 654 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 666 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 656 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 664 " --> pdb=" O ARG A 656 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 679 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.607A pdb=" N ILE A1554 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 831 removed outlier: 5.599A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.550A pdb=" N VAL A 776 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 826 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR A 778 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 865 through 867 Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 934 removed outlier: 4.369A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 949 through 951 removed outlier: 3.837A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A1031 " --> pdb=" O VAL A 990 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3715 1.34 - 1.46: 3029 1.46 - 1.58: 5584 1.58 - 1.71: 114 1.71 - 1.83: 83 Bond restraints: 12525 Sorted by residual: bond pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N VAL A 625 " pdb=" CA VAL A 625 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.76e+00 bond pdb=" N VAL A 373 " pdb=" CA VAL A 373 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.64e+00 bond pdb=" N ASP A 620 " pdb=" CA ASP A 620 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.23e-02 6.61e+03 8.35e+00 bond pdb=" N HIS A 289 " pdb=" CA HIS A 289 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.77e+00 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 16905 2.91 - 5.82: 304 5.82 - 8.72: 32 8.72 - 11.63: 3 11.63 - 14.54: 2 Bond angle restraints: 17246 Sorted by residual: angle pdb=" N ARG A1895 " pdb=" CA ARG A1895 " pdb=" C ARG A1895 " ideal model delta sigma weight residual 114.56 108.26 6.30 1.27e+00 6.20e-01 2.46e+01 angle pdb=" CB MET A1808 " pdb=" CG MET A1808 " pdb=" SD MET A1808 " ideal model delta sigma weight residual 112.70 126.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " pdb=" CG LYS A 862 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 angle pdb=" CA LYS A 584 " pdb=" CB LYS A 584 " pdb=" CG LYS A 584 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 angle pdb=" C LEU A 370 " pdb=" CA LEU A 370 " pdb=" CB LEU A 370 " ideal model delta sigma weight residual 116.63 111.65 4.98 1.16e+00 7.43e-01 1.84e+01 ... (remaining 17241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6485 17.80 - 35.60: 813 35.60 - 53.39: 285 53.39 - 71.19: 120 71.19 - 88.99: 28 Dihedral angle restraints: 7731 sinusoidal: 3717 harmonic: 4014 Sorted by residual: dihedral pdb=" CA ILE A 149 " pdb=" C ILE A 149 " pdb=" N MET A 150 " pdb=" CA MET A 150 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA MET A 684 " pdb=" C MET A 684 " pdb=" N SER A 685 " pdb=" CA SER A 685 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA THR A 915 " pdb=" C THR A 915 " pdb=" N LYS A 916 " pdb=" CA LYS A 916 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1899 0.107 - 0.214: 85 0.214 - 0.321: 2 0.321 - 0.428: 0 0.428 - 0.535: 7 Chirality restraints: 1993 Sorted by residual: chirality pdb=" P G B 26 " pdb=" OP1 G B 26 " pdb=" OP2 G B 26 " pdb=" O5' G B 26 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" P G B 60 " pdb=" OP1 G B 60 " pdb=" OP2 G B 60 " pdb=" O5' G B 60 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" P G B 58 " pdb=" OP1 G B 58 " pdb=" OP2 G B 58 " pdb=" O5' G B 58 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 1990 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 960 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO A 961 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 961 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 961 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 184 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO A 185 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1376 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A1377 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " 0.033 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 194 2.60 - 3.17: 11093 3.17 - 3.75: 20768 3.75 - 4.32: 27573 4.32 - 4.90: 43090 Nonbonded interactions: 102718 Sorted by model distance: nonbonded pdb=" O TYR A1330 " pdb=" OG1 THR A1334 " model vdw 2.021 3.040 nonbonded pdb=" OG1 THR A1074 " pdb=" OH TYR A1570 " model vdw 2.034 3.040 nonbonded pdb=" O GLU A 391 " pdb=" OH TYR A 473 " model vdw 2.035 3.040 nonbonded pdb=" O ARG A 739 " pdb=" OG SER A 742 " model vdw 2.045 3.040 nonbonded pdb=" O PRO A 956 " pdb=" OG1 THR A 967 " model vdw 2.053 3.040 ... (remaining 102713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 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 : 0.005 0.081 12526 Z= 0.268 Angle : 0.885 14.539 17248 Z= 0.484 Chirality : 0.055 0.535 1993 Planarity : 0.006 0.076 1994 Dihedral : 19.060 88.988 5126 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.33 % Allowed : 28.78 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.23), residues: 1343 helix: 0.34 (0.22), residues: 567 sheet: -2.89 (0.47), residues: 100 loop : -1.92 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 789 TYR 0.031 0.002 TYR A1834 PHE 0.017 0.001 PHE A1812 TRP 0.009 0.002 TRP A1831 HIS 0.007 0.001 HIS A1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.27 (12525) covalent geometry : angle 0.88519 / 0.48 (17246) SS BOND : bond 0.00569 / 0.38 ( 1) SS BOND : angle 2.00233 / 1.20 ( 2) hydrogen bonds : bond 0.15586 / 10.06 ( 515) hydrogen bonds : angle 6.57141 / 4.67 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 TYR cc_start: 0.5996 (t80) cc_final: 0.5743 (t80) REVERT: A 684 MET cc_start: 0.2799 (ppp) cc_final: 0.2339 (ppp) REVERT: A 1861 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5706 (tp30) outliers start: 53 outliers final: 40 residues processed: 187 average time/residue: 0.4465 time to fit residues: 91.5865 Evaluate side-chains 163 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN A1379 ASN A1660 ASN A1719 HIS A1727 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.181733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.159101 restraints weight = 33074.258| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 2.12 r_work: 0.4375 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12526 Z= 0.160 Angle : 0.708 12.016 17248 Z= 0.362 Chirality : 0.044 0.208 1993 Planarity : 0.006 0.061 1994 Dihedral : 15.751 80.120 2447 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.79 % Allowed : 24.28 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.23), residues: 1343 helix: 0.31 (0.21), residues: 576 sheet: -3.10 (0.42), residues: 113 loop : -1.92 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 688 TYR 0.020 0.002 TYR A 560 PHE 0.017 0.001 PHE A1706 TRP 0.023 0.003 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (12525) covalent geometry : angle 0.70838 / 0.36 (17246) SS BOND : bond 0.00088 / 0.06 ( 1) SS BOND : angle 0.53248 / 0.29 ( 2) hydrogen bonds : bond 0.05610 / 3.73 ( 515) hydrogen bonds : angle 5.49109 / 3.84 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 142 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 HIS cc_start: 0.5210 (OUTLIER) cc_final: 0.4808 (m90) REVERT: A 763 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7191 (mpt-90) REVERT: A 775 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5878 (mpp) REVERT: A 859 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5221 (mtt90) REVERT: A 1337 ASP cc_start: 0.6747 (t0) cc_final: 0.6434 (p0) REVERT: A 1803 GLU cc_start: 0.4424 (OUTLIER) cc_final: 0.3951 (pp20) outliers start: 83 outliers final: 40 residues processed: 216 average time/residue: 0.4811 time to fit residues: 113.1682 Evaluate side-chains 175 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 859 ARG Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1304 SER Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1803 GLU Chi-restraints excluded: chain A residue 1837 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 488 GLN A1660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.180518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.157617 restraints weight = 33141.028| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 2.15 r_work: 0.4358 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12526 Z= 0.165 Angle : 0.704 12.725 17248 Z= 0.357 Chirality : 0.044 0.227 1993 Planarity : 0.006 0.059 1994 Dihedral : 15.597 79.355 2429 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.52 % Allowed : 26.49 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1343 helix: 0.28 (0.21), residues: 572 sheet: -2.94 (0.45), residues: 98 loop : -1.80 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 789 TYR 0.021 0.002 TYR A1357 PHE 0.017 0.002 PHE A1706 TRP 0.016 0.002 TRP A 316 HIS 0.004 0.001 HIS A1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (12525) covalent geometry : angle 0.70374 / 0.36 (17246) SS BOND : bond 0.00119 / 0.08 ( 1) SS BOND : angle 0.62129 / 0.34 ( 2) hydrogen bonds : bond 0.05326 / 3.53 ( 515) hydrogen bonds : angle 5.37844 / 3.77 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 144 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2815 (OUTLIER) cc_final: 0.2492 (mp) REVERT: A 486 LYS cc_start: -0.3472 (OUTLIER) cc_final: -0.3813 (pttp) REVERT: A 500 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8308 (tmtt) REVERT: A 563 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5227 (mt) REVERT: A 649 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5267 (tm) REVERT: A 711 HIS cc_start: 0.5695 (OUTLIER) cc_final: 0.5342 (m90) REVERT: A 775 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5903 (mpp) REVERT: A 1337 ASP cc_start: 0.7203 (t0) cc_final: 0.6733 (p0) REVERT: A 1803 GLU cc_start: 0.4974 (OUTLIER) cc_final: 0.4367 (pp20) outliers start: 92 outliers final: 41 residues processed: 218 average time/residue: 0.4884 time to fit residues: 116.0792 Evaluate side-chains 180 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 121 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 488 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.181828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.159088 restraints weight = 33257.313| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 2.16 r_work: 0.4367 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12526 Z= 0.141 Angle : 0.686 10.081 17248 Z= 0.349 Chirality : 0.043 0.207 1993 Planarity : 0.005 0.057 1994 Dihedral : 15.469 78.607 2424 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 6.70 % Allowed : 26.98 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1343 helix: 0.35 (0.21), residues: 575 sheet: -2.93 (0.46), residues: 100 loop : -1.74 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 688 TYR 0.020 0.002 TYR A1714 PHE 0.022 0.001 PHE A 922 TRP 0.022 0.002 TRP A 316 HIS 0.005 0.001 HIS A1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12525) covalent geometry : angle 0.68649 / 0.35 (17246) SS BOND : bond 0.00149 / 0.10 ( 1) SS BOND : angle 0.42729 / 0.25 ( 2) hydrogen bonds : bond 0.04939 / 3.26 ( 515) hydrogen bonds : angle 5.20397 / 3.66 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 137 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2323 (OUTLIER) cc_final: 0.1997 (mp) REVERT: A 486 LYS cc_start: -0.3479 (OUTLIER) cc_final: -0.3787 (pttp) REVERT: A 500 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8060 (tptt) REVERT: A 507 LYS cc_start: 0.8009 (pttt) cc_final: 0.7613 (pptt) REVERT: A 636 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.5150 (mtm110) REVERT: A 649 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4984 (tm) REVERT: A 711 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.4825 (m90) REVERT: A 775 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5896 (mpp) REVERT: A 842 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6373 (ttm) REVERT: A 865 LEU cc_start: 0.6627 (mt) cc_final: 0.6370 (mt) REVERT: A 1337 ASP cc_start: 0.6864 (t0) cc_final: 0.6510 (p0) REVERT: A 1381 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6786 (pt) REVERT: A 1803 GLU cc_start: 0.4423 (OUTLIER) cc_final: 0.3901 (pp20) outliers start: 82 outliers final: 39 residues processed: 208 average time/residue: 0.4690 time to fit residues: 106.6937 Evaluate side-chains 181 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.180594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.157517 restraints weight = 32965.245| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.13 r_work: 0.4348 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12526 Z= 0.161 Angle : 0.699 8.932 17248 Z= 0.357 Chirality : 0.044 0.327 1993 Planarity : 0.005 0.057 1994 Dihedral : 15.415 78.016 2420 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 7.11 % Allowed : 27.56 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.22), residues: 1343 helix: 0.32 (0.21), residues: 575 sheet: -2.95 (0.49), residues: 95 loop : -1.75 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1358 TYR 0.022 0.002 TYR A1357 PHE 0.017 0.001 PHE A1706 TRP 0.024 0.003 TRP A 316 HIS 0.011 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (12525) covalent geometry : angle 0.69862 / 0.36 (17246) SS BOND : bond 0.00133 / 0.09 ( 1) SS BOND : angle 0.38609 / 0.22 ( 2) hydrogen bonds : bond 0.04953 / 3.28 ( 515) hydrogen bonds : angle 5.19491 / 3.65 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 136 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ILE cc_start: 0.5257 (mp) cc_final: 0.4802 (mp) REVERT: A 205 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1771 (mp) REVERT: A 230 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 500 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8060 (tptt) REVERT: A 507 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7597 (pptt) REVERT: A 649 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5103 (tm) REVERT: A 775 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5874 (mpp) REVERT: A 865 LEU cc_start: 0.6723 (mt) cc_final: 0.6443 (mt) REVERT: A 1337 ASP cc_start: 0.6796 (t0) cc_final: 0.6557 (p0) REVERT: A 1381 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6979 (pt) REVERT: A 1803 GLU cc_start: 0.4415 (OUTLIER) cc_final: 0.3903 (pp20) outliers start: 87 outliers final: 50 residues processed: 210 average time/residue: 0.4704 time to fit residues: 108.4368 Evaluate side-chains 194 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS A 672 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN A1668 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.180299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.156854 restraints weight = 32974.311| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 2.16 r_work: 0.4336 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12526 Z= 0.174 Angle : 0.735 9.648 17248 Z= 0.373 Chirality : 0.044 0.283 1993 Planarity : 0.006 0.058 1994 Dihedral : 15.425 77.670 2420 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 6.54 % Allowed : 29.03 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.22), residues: 1343 helix: 0.21 (0.21), residues: 573 sheet: -2.91 (0.49), residues: 95 loop : -1.72 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 688 TYR 0.028 0.002 TYR A 637 PHE 0.019 0.002 PHE A 498 TRP 0.026 0.003 TRP A 316 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (12525) covalent geometry : angle 0.73514 / 0.37 (17246) SS BOND : bond 0.00167 / 0.11 ( 1) SS BOND : angle 0.36656 / 0.21 ( 2) hydrogen bonds : bond 0.05105 / 3.34 ( 515) hydrogen bonds : angle 5.23051 / 3.67 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 141 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2162 (OUTLIER) cc_final: 0.1758 (mp) REVERT: A 230 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 499 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.8020 (ptp-110) REVERT: A 500 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8274 (tmtt) REVERT: A 507 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7440 (pptt) REVERT: A 636 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5158 (mtm110) REVERT: A 649 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5293 (tm) REVERT: A 672 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7266 (p0) REVERT: A 775 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.6080 (mpp) REVERT: A 836 PHE cc_start: 0.2334 (OUTLIER) cc_final: 0.1479 (p90) REVERT: A 865 LEU cc_start: 0.6714 (mt) cc_final: 0.6398 (mt) REVERT: A 1337 ASP cc_start: 0.6858 (t0) cc_final: 0.6649 (p0) REVERT: A 1357 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 1381 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6970 (pt) REVERT: A 1668 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6770 (t0) REVERT: A 1803 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.3944 (pp20) outliers start: 80 outliers final: 48 residues processed: 207 average time/residue: 0.4776 time to fit residues: 107.9327 Evaluate side-chains 189 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 128 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.180517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.157295 restraints weight = 32861.224| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.15 r_work: 0.4347 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12526 Z= 0.155 Angle : 0.732 10.551 17248 Z= 0.370 Chirality : 0.044 0.300 1993 Planarity : 0.005 0.059 1994 Dihedral : 15.376 77.532 2419 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.38 % Allowed : 30.17 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1343 helix: 0.24 (0.21), residues: 574 sheet: -2.96 (0.44), residues: 110 loop : -1.72 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 688 TYR 0.023 0.002 TYR A1714 PHE 0.019 0.001 PHE A 894 TRP 0.027 0.003 TRP A 316 HIS 0.010 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (12525) covalent geometry : angle 0.73190 / 0.37 (17246) SS BOND : bond 0.00147 / 0.10 ( 1) SS BOND : angle 0.28967 / 0.17 ( 2) hydrogen bonds : bond 0.04921 / 3.24 ( 515) hydrogen bonds : angle 5.21653 / 3.66 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 135 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2567 (OUTLIER) cc_final: 0.2139 (mp) REVERT: A 230 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7971 (mp) REVERT: A 499 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.8007 (ptp-110) REVERT: A 500 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8312 (tmtt) REVERT: A 507 LYS cc_start: 0.7970 (pttt) cc_final: 0.7463 (pptt) REVERT: A 836 PHE cc_start: 0.2595 (OUTLIER) cc_final: 0.1697 (p90) REVERT: A 842 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6329 (tpp) REVERT: A 865 LEU cc_start: 0.6705 (mt) cc_final: 0.6416 (mt) REVERT: A 1337 ASP cc_start: 0.7085 (t0) cc_final: 0.6769 (p0) REVERT: A 1381 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6947 (OUTLIER) REVERT: A 1660 ASN cc_start: 0.4643 (m-40) cc_final: 0.4409 (m110) REVERT: A 1803 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4387 (pp20) outliers start: 78 outliers final: 48 residues processed: 197 average time/residue: 0.4567 time to fit residues: 98.3221 Evaluate side-chains 185 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Chi-restraints excluded: chain A residue 1803 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 672 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.178399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.154549 restraints weight = 32701.403| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.13 r_work: 0.4299 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12526 Z= 0.226 Angle : 0.819 14.568 17248 Z= 0.414 Chirality : 0.048 0.324 1993 Planarity : 0.007 0.087 1994 Dihedral : 15.521 77.691 2417 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 6.30 % Allowed : 30.91 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1343 helix: -0.08 (0.21), residues: 574 sheet: -3.00 (0.45), residues: 108 loop : -1.78 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 636 TYR 0.031 0.003 TYR A 637 PHE 0.020 0.002 PHE A1706 TRP 0.035 0.004 TRP A 316 HIS 0.012 0.002 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (12525) covalent geometry : angle 0.81946 / 0.41 (17246) SS BOND : bond 0.00329 / 0.22 ( 1) SS BOND : angle 0.71484 / 0.38 ( 2) hydrogen bonds : bond 0.05364 / 3.51 ( 515) hydrogen bonds : angle 5.42357 / 3.80 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 137 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: A 205 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.2271 (mp) REVERT: A 230 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 390 TYR cc_start: 0.7225 (t80) cc_final: 0.7010 (t80) REVERT: A 500 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8332 (tmtt) REVERT: A 507 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7522 (pptt) REVERT: A 672 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7369 (p0) REVERT: A 788 ARG cc_start: 0.4173 (OUTLIER) cc_final: 0.3946 (ppt-90) REVERT: A 836 PHE cc_start: 0.2883 (OUTLIER) cc_final: 0.1802 (p90) REVERT: A 842 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6517 (tpp) REVERT: A 1337 ASP cc_start: 0.7190 (t0) cc_final: 0.6989 (p0) REVERT: A 1350 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7813 (mtmm) REVERT: A 1381 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7040 (pt) REVERT: A 1660 ASN cc_start: 0.4724 (m-40) cc_final: 0.4503 (m110) REVERT: A 1668 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6969 (t0) REVERT: A 1732 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6528 (mp) outliers start: 77 outliers final: 45 residues processed: 201 average time/residue: 0.4879 time to fit residues: 106.9495 Evaluate side-chains 191 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1762 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 GLN ** A1062 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 = 0.4809 r_free = 0.4809 target = 0.179326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.155996 restraints weight = 32714.959| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.11 r_work: 0.4328 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12526 Z= 0.168 Angle : 0.790 12.730 17248 Z= 0.398 Chirality : 0.045 0.283 1993 Planarity : 0.006 0.059 1994 Dihedral : 15.455 78.018 2412 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.48 % Allowed : 31.73 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.22), residues: 1343 helix: 0.03 (0.21), residues: 572 sheet: -3.00 (0.45), residues: 110 loop : -1.77 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 688 TYR 0.025 0.002 TYR A1714 PHE 0.017 0.001 PHE A1706 TRP 0.038 0.003 TRP A 316 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12525) covalent geometry : angle 0.78993 / 0.40 (17246) SS BOND : bond 0.00258 / 0.17 ( 1) SS BOND : angle 0.40324 / 0.21 ( 2) hydrogen bonds : bond 0.05054 / 3.32 ( 515) hydrogen bonds : angle 5.35311 / 3.75 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2283 (mp) REVERT: A 230 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 390 TYR cc_start: 0.7140 (t80) cc_final: 0.6716 (t80) REVERT: A 499 ARG cc_start: 0.8181 (ptp-110) cc_final: 0.7967 (ptp-110) REVERT: A 500 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8402 (tmtt) REVERT: A 507 LYS cc_start: 0.7972 (pttt) cc_final: 0.7494 (pptt) REVERT: A 836 PHE cc_start: 0.2981 (OUTLIER) cc_final: 0.2027 (p90) REVERT: A 842 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6453 (tpp) REVERT: A 996 ARG cc_start: 0.7015 (pmt-80) cc_final: 0.6649 (ppt170) REVERT: A 1337 ASP cc_start: 0.7128 (t0) cc_final: 0.6901 (p0) REVERT: A 1350 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7862 (mtmm) REVERT: A 1357 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6365 (t80) REVERT: A 1381 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6939 (pt) REVERT: A 1660 ASN cc_start: 0.4787 (m-40) cc_final: 0.4566 (m110) outliers start: 67 outliers final: 44 residues processed: 198 average time/residue: 0.4859 time to fit residues: 104.9613 Evaluate side-chains 188 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 52 optimal weight: 0.0870 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.180515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.157373 restraints weight = 33189.778| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 2.15 r_work: 0.4360 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4243 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12526 Z= 0.158 Angle : 0.817 13.018 17248 Z= 0.410 Chirality : 0.045 0.274 1993 Planarity : 0.006 0.060 1994 Dihedral : 15.366 77.420 2412 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 33.03 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.22), residues: 1343 helix: 0.14 (0.21), residues: 570 sheet: -2.90 (0.47), residues: 103 loop : -1.81 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 688 TYR 0.027 0.002 TYR A1357 PHE 0.032 0.002 PHE A 894 TRP 0.054 0.003 TRP A 316 HIS 0.007 0.001 HIS A1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (12525) covalent geometry : angle 0.81704 / 0.41 (17246) SS BOND : bond 0.00256 / 0.17 ( 1) SS BOND : angle 0.28017 / 0.15 ( 2) hydrogen bonds : bond 0.04985 / 3.25 ( 515) hydrogen bonds : angle 5.31102 / 3.74 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.2249 (mp) REVERT: A 230 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 390 TYR cc_start: 0.7026 (t80) cc_final: 0.6687 (m-80) REVERT: A 499 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7926 (ptp-110) REVERT: A 507 LYS cc_start: 0.7968 (pttt) cc_final: 0.7506 (pptt) REVERT: A 812 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 842 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6592 (ttm) REVERT: A 996 ARG cc_start: 0.7019 (pmt-80) cc_final: 0.6705 (ppt170) REVERT: A 1337 ASP cc_start: 0.7076 (t0) cc_final: 0.6817 (p0) REVERT: A 1381 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6837 (pt) REVERT: A 1660 ASN cc_start: 0.4928 (m-40) cc_final: 0.4713 (m110) outliers start: 52 outliers final: 37 residues processed: 177 average time/residue: 0.5968 time to fit residues: 115.2274 Evaluate side-chains 164 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1762 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.179463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.156116 restraints weight = 32622.757| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.12 r_work: 0.4344 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12526 Z= 0.173 Angle : 0.803 12.918 17248 Z= 0.405 Chirality : 0.046 0.286 1993 Planarity : 0.006 0.078 1994 Dihedral : 15.302 77.422 2406 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 33.12 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1343 helix: 0.03 (0.21), residues: 576 sheet: -2.88 (0.47), residues: 98 loop : -1.82 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 789 TYR 0.025 0.002 TYR A1714 PHE 0.015 0.002 PHE A1706 TRP 0.052 0.004 TRP A 316 HIS 0.006 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (12525) covalent geometry : angle 0.80285 / 0.40 (17246) SS BOND : bond 0.00167 / 0.11 ( 1) SS BOND : angle 0.32720 / 0.18 ( 2) hydrogen bonds : bond 0.05017 / 3.28 ( 515) hydrogen bonds : angle 5.33626 / 3.75 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3837.69 seconds wall clock time: 66 minutes 23.11 seconds (3983.11 seconds total)