Starting phenix.real_space_refine on Sun Apr 5 18:24:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cb_67570/04_2026/21cb_67570.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cb_67570/04_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_67570/04_2026/21cb_67570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cb_67570/04_2026/21cb_67570.map" model { file = "/net/cci-nas-00/data/ceres_data/21cb_67570/04_2026/21cb_67570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cb_67570/04_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-2.1rc1-6017/lib/python3.9/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: 2.62, per 1000 atoms: 0.22 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: 0.96 Conformation dependent library (CDL) restraints added in 500.9 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: 1.55 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: 2.83 Time building geometry restraints manager: 1.25 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: 1.040 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.000 Find NCS groups from input model: 0.030 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:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 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= 0.263 Angle : 0.885 14.539 17248 Z= 0.470 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 covalent geometry : bond 0.00523 (12525) covalent geometry : angle 0.88518 (17246) SS BOND : bond 0.00569 ( 1) SS BOND : angle 2.00233 ( 2) hydrogen bonds : bond 0.15586 ( 515) hydrogen bonds : angle 6.57141 ( 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 : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.5182 time to fit residues: 105.8118 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 : 0.318 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A1073 GLN A1379 ASN A1660 ASN A1719 HIS A1727 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.181424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.158825 restraints weight = 32935.691| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.12 r_work: 0.4369 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12526 Z= 0.147 Angle : 0.675 12.459 17248 Z= 0.341 Chirality : 0.043 0.239 1993 Planarity : 0.006 0.065 1994 Dihedral : 15.583 78.433 2447 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 7.28 % Allowed : 23.63 % Favored : 69.09 % 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 (0.23), residues: 1343 helix: 0.43 (0.21), residues: 573 sheet: -3.02 (0.46), residues: 100 loop : -1.79 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 789 TYR 0.021 0.002 TYR A1357 PHE 0.015 0.001 PHE A1666 TRP 0.020 0.002 TRP A 316 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00345 (12525) covalent geometry : angle 0.67487 (17246) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.60388 ( 2) hydrogen bonds : bond 0.04855 ( 515) hydrogen bonds : angle 5.23915 ( 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 235 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 146 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.6517 (tpt) cc_final: 0.6255 (tpt) REVERT: A 349 ASP cc_start: 0.5239 (m-30) cc_final: 0.4878 (m-30) REVERT: A 486 LYS cc_start: -0.3324 (OUTLIER) cc_final: -0.3628 (pttp) REVERT: A 500 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8231 (tmtt) REVERT: A 563 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5127 (mt) REVERT: A 711 HIS cc_start: 0.5268 (OUTLIER) cc_final: 0.4889 (m90) REVERT: A 775 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.6036 (mpp) REVERT: A 865 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6257 (mt) REVERT: A 1337 ASP cc_start: 0.6861 (t0) cc_final: 0.6555 (p0) REVERT: A 1357 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.5844 (t80) REVERT: A 1381 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6963 (pt) REVERT: A 1803 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.3919 (pp20) outliers start: 89 outliers final: 33 residues processed: 219 average time/residue: 0.5517 time to fit residues: 131.2397 Evaluate side-chains 170 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 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 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 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 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 627 ILE 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 775 MET Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 865 LEU 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 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** 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 = 0.4833 r_free = 0.4833 target = 0.180874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.158154 restraints weight = 33157.224| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 2.14 r_work: 0.4355 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12526 Z= 0.147 Angle : 0.666 9.636 17248 Z= 0.337 Chirality : 0.043 0.214 1993 Planarity : 0.006 0.062 1994 Dihedral : 15.336 77.194 2424 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.79 % Allowed : 25.76 % Favored : 67.46 % 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: -1.28 (0.23), residues: 1343 helix: 0.44 (0.21), residues: 576 sheet: -2.84 (0.49), residues: 95 loop : -1.72 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 789 TYR 0.020 0.002 TYR A1714 PHE 0.018 0.001 PHE A 922 TRP 0.024 0.002 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00342 (12525) covalent geometry : angle 0.66648 (17246) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.28586 ( 2) hydrogen bonds : bond 0.04668 ( 515) hydrogen bonds : angle 5.09823 ( 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 222 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 139 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1921 (mp) REVERT: A 324 MET cc_start: 0.6644 (tpt) cc_final: 0.6296 (tpt) REVERT: A 349 ASP cc_start: 0.4882 (m-30) cc_final: 0.4618 (m-30) REVERT: A 442 LEU cc_start: 0.0675 (OUTLIER) cc_final: 0.0455 (mp) REVERT: A 507 LYS cc_start: 0.7841 (pttt) cc_final: 0.7543 (pptt) REVERT: A 775 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5931 (mpp) REVERT: A 1337 ASP cc_start: 0.6846 (t0) cc_final: 0.6584 (p0) REVERT: A 1381 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6907 (pt) REVERT: A 1803 GLU cc_start: 0.4434 (OUTLIER) cc_final: 0.3932 (pp20) outliers start: 83 outliers final: 33 residues processed: 208 average time/residue: 0.5284 time to fit residues: 119.4855 Evaluate side-chains 171 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 97 VAL 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 238 THR Chi-restraints excluded: chain A residue 240 LEU 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 442 LEU 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 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 953 ASP 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 1066 THR 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 1803 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 GLN A1660 ASN A1668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.181411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.158507 restraints weight = 33056.216| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 2.19 r_work: 0.4366 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12526 Z= 0.139 Angle : 0.671 8.930 17248 Z= 0.339 Chirality : 0.043 0.272 1993 Planarity : 0.005 0.061 1994 Dihedral : 15.235 76.665 2418 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.81 % Allowed : 27.96 % Favored : 66.23 % 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: -1.20 (0.23), residues: 1343 helix: 0.45 (0.21), residues: 576 sheet: -2.71 (0.49), residues: 100 loop : -1.62 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 789 TYR 0.022 0.002 TYR A1714 PHE 0.015 0.001 PHE A 894 TRP 0.024 0.002 TRP A 316 HIS 0.008 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00328 (12525) covalent geometry : angle 0.67127 (17246) SS BOND : bond 0.00301 ( 1) SS BOND : angle 0.32218 ( 2) hydrogen bonds : bond 0.04553 ( 515) hydrogen bonds : angle 4.99663 ( 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 213 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2285 (OUTLIER) cc_final: 0.1685 (mp) REVERT: A 324 MET cc_start: 0.6779 (tpt) cc_final: 0.6415 (tpt) REVERT: A 349 ASP cc_start: 0.4675 (m-30) cc_final: 0.4405 (m-30) REVERT: A 499 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7905 (ptp-110) REVERT: A 507 LYS cc_start: 0.7833 (pttt) cc_final: 0.7443 (pptt) REVERT: A 836 PHE cc_start: 0.2308 (OUTLIER) cc_final: 0.1506 (p90) REVERT: A 865 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6439 (mt) REVERT: A 1337 ASP cc_start: 0.6836 (t0) cc_final: 0.6564 (p0) outliers start: 71 outliers final: 32 residues processed: 202 average time/residue: 0.5244 time to fit residues: 115.4767 Evaluate side-chains 167 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 138 TRP 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 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 390 TYR 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 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR 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 843 LEU 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 1311 ASN Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 76 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A1660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.181605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.158711 restraints weight = 33110.441| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.18 r_work: 0.4379 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12526 Z= 0.136 Angle : 0.676 9.158 17248 Z= 0.340 Chirality : 0.043 0.256 1993 Planarity : 0.005 0.061 1994 Dihedral : 15.072 76.189 2407 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.56 % Allowed : 28.95 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.18 (0.23), residues: 1343 helix: 0.52 (0.21), residues: 574 sheet: -2.72 (0.49), residues: 100 loop : -1.65 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 789 TYR 0.020 0.002 TYR A1714 PHE 0.021 0.001 PHE A 867 TRP 0.026 0.002 TRP A 316 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00317 (12525) covalent geometry : angle 0.67636 (17246) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.56286 ( 2) hydrogen bonds : bond 0.04412 ( 515) hydrogen bonds : angle 4.91790 ( 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 205 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2240 (OUTLIER) cc_final: 0.1693 (mp) REVERT: A 324 MET cc_start: 0.6766 (tpt) cc_final: 0.6348 (tpt) REVERT: A 349 ASP cc_start: 0.4909 (m-30) cc_final: 0.4499 (m-30) REVERT: A 507 LYS cc_start: 0.7718 (pttt) cc_final: 0.7210 (pptt) REVERT: A 836 PHE cc_start: 0.2239 (OUTLIER) cc_final: 0.1436 (p90) REVERT: A 865 LEU cc_start: 0.6668 (mt) cc_final: 0.6388 (mt) REVERT: A 1337 ASP cc_start: 0.6861 (t0) cc_final: 0.6610 (p0) outliers start: 68 outliers final: 34 residues processed: 197 average time/residue: 0.5119 time to fit residues: 109.8538 Evaluate side-chains 169 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR 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 390 TYR 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 668 TYR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 734 THR 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 843 LEU Chi-restraints excluded: chain A residue 853 ILE 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 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1715 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN A 672 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 ASN A1660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.153296 restraints weight = 32480.346| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.10 r_work: 0.4286 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12526 Z= 0.239 Angle : 0.815 10.755 17248 Z= 0.410 Chirality : 0.048 0.284 1993 Planarity : 0.006 0.062 1994 Dihedral : 15.325 81.107 2404 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 6.62 % Allowed : 29.03 % Favored : 64.35 % 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: -1.79 (0.22), residues: 1343 helix: -0.08 (0.21), residues: 574 sheet: -2.99 (0.42), residues: 108 loop : -1.87 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 688 TYR 0.028 0.003 TYR A1714 PHE 0.019 0.002 PHE A1706 TRP 0.033 0.004 TRP A 316 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00583 (12525) covalent geometry : angle 0.81479 (17246) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.62953 ( 2) hydrogen bonds : bond 0.05225 ( 515) hydrogen bonds : angle 5.43559 ( 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 234 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.7441 (t) cc_final: 0.7051 (m) REVERT: A 84 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6028 (pp30) REVERT: A 124 TYR cc_start: 0.5865 (m-80) cc_final: 0.5311 (m-10) REVERT: A 205 LEU cc_start: 0.2790 (OUTLIER) cc_final: 0.2341 (mp) REVERT: A 324 MET cc_start: 0.6893 (tpt) cc_final: 0.6479 (tpt) REVERT: A 349 ASP cc_start: 0.4905 (m-30) cc_final: 0.4569 (m-30) REVERT: A 499 ARG cc_start: 0.8075 (ptp-110) cc_final: 0.7866 (ptp-110) REVERT: A 507 LYS cc_start: 0.7788 (pttt) cc_final: 0.7387 (pptt) REVERT: A 672 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7416 (p0) REVERT: A 832 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8026 (mtpt) REVERT: A 836 PHE cc_start: 0.3408 (OUTLIER) cc_final: 0.2243 (p90) REVERT: A 837 MET cc_start: 0.1498 (mmp) cc_final: 0.0477 (mmp) REVERT: A 895 LYS cc_start: 0.8377 (tmmm) cc_final: 0.8007 (tmmm) outliers start: 81 outliers final: 37 residues processed: 222 average time/residue: 0.5227 time to fit residues: 126.4126 Evaluate side-chains 176 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 GLN 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 238 THR 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 521 ILE Chi-restraints excluded: chain A residue 614 TYR 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 698 CYS Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 832 LYS Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 874 SER 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 1311 ASN Chi-restraints excluded: chain A residue 1320 ASP 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 1837 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.179539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.156550 restraints weight = 32782.890| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.07 r_work: 0.4327 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12526 Z= 0.160 Angle : 0.759 14.316 17248 Z= 0.378 Chirality : 0.045 0.264 1993 Planarity : 0.006 0.060 1994 Dihedral : 15.135 78.224 2402 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.23 % Allowed : 31.15 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.22), residues: 1343 helix: 0.03 (0.21), residues: 575 sheet: -2.78 (0.47), residues: 98 loop : -1.81 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 688 TYR 0.024 0.002 TYR A1714 PHE 0.026 0.002 PHE A 498 TRP 0.033 0.003 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00379 (12525) covalent geometry : angle 0.75924 (17246) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.56626 ( 2) hydrogen bonds : bond 0.04677 ( 515) hydrogen bonds : angle 5.26707 ( 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 204 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.7076 (t) cc_final: 0.6853 (m) REVERT: A 205 LEU cc_start: 0.2807 (OUTLIER) cc_final: 0.2196 (mp) REVERT: A 349 ASP cc_start: 0.4855 (m-30) cc_final: 0.4399 (m-30) REVERT: A 499 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7873 (ptp-110) REVERT: A 507 LYS cc_start: 0.7723 (pttt) cc_final: 0.7334 (pptt) REVERT: A 791 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7261 (mtmm) REVERT: A 836 PHE cc_start: 0.3269 (OUTLIER) cc_final: 0.2290 (p90) REVERT: A 837 MET cc_start: 0.1717 (mmp) cc_final: 0.0528 (mmp) REVERT: A 865 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6241 (mp) REVERT: A 996 ARG cc_start: 0.7099 (pmt-80) cc_final: 0.6801 (ppt170) outliers start: 64 outliers final: 32 residues processed: 194 average time/residue: 0.5624 time to fit residues: 118.2707 Evaluate side-chains 171 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR 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 476 SER Chi-restraints excluded: chain A residue 614 TYR 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 791 LYS 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 865 LEU Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 920 PHE 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 1311 ASN Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1837 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN A 672 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.178465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.155092 restraints weight = 32723.239| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.17 r_work: 0.4317 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12526 Z= 0.175 Angle : 0.791 14.031 17248 Z= 0.392 Chirality : 0.046 0.272 1993 Planarity : 0.006 0.062 1994 Dihedral : 15.118 78.743 2400 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.50 % Allowed : 32.46 % Favored : 63.04 % 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: -0.01 (0.21), residues: 575 sheet: -2.89 (0.46), residues: 98 loop : -1.79 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 789 TYR 0.028 0.002 TYR A 914 PHE 0.020 0.002 PHE A 894 TRP 0.036 0.003 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00417 (12525) covalent geometry : angle 0.79072 (17246) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.60700 ( 2) hydrogen bonds : bond 0.04692 ( 515) hydrogen bonds : angle 5.25728 ( 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 192 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.7093 (t) cc_final: 0.6860 (m) REVERT: A 124 TYR cc_start: 0.5565 (m-80) cc_final: 0.5256 (m-10) REVERT: A 205 LEU cc_start: 0.2217 (OUTLIER) cc_final: 0.1673 (mp) REVERT: A 349 ASP cc_start: 0.4541 (m-30) cc_final: 0.4296 (m-30) REVERT: A 507 LYS cc_start: 0.7632 (pttt) cc_final: 0.7250 (pptt) REVERT: A 533 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5302 (mt) REVERT: A 791 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7264 (mtmm) REVERT: A 836 PHE cc_start: 0.2902 (OUTLIER) cc_final: 0.1867 (p90) outliers start: 55 outliers final: 37 residues processed: 184 average time/residue: 0.5360 time to fit residues: 107.5385 Evaluate side-chains 177 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR 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 158 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR 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 476 SER Chi-restraints excluded: chain A residue 533 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 791 LYS 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 865 LEU Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 902 LYS 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 1032 ILE 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 1569 CYS Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1837 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** 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 = 0.4824 r_free = 0.4824 target = 0.180524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.157978 restraints weight = 32744.798| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.09 r_work: 0.4377 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12526 Z= 0.145 Angle : 0.775 14.006 17248 Z= 0.380 Chirality : 0.044 0.278 1993 Planarity : 0.005 0.061 1994 Dihedral : 14.933 77.580 2398 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.76 % Allowed : 33.12 % Favored : 63.12 % 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: 0.12 (0.21), residues: 582 sheet: -2.74 (0.50), residues: 91 loop : -1.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 789 TYR 0.028 0.002 TYR A 914 PHE 0.034 0.001 PHE A 867 TRP 0.039 0.003 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00336 (12525) covalent geometry : angle 0.77479 (17246) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.86841 ( 2) hydrogen bonds : bond 0.04444 ( 515) hydrogen bonds : angle 5.11295 ( 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 183 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2578 (OUTLIER) cc_final: 0.1962 (mp) REVERT: A 349 ASP cc_start: 0.4545 (m-30) cc_final: 0.4094 (m-30) REVERT: A 507 LYS cc_start: 0.7712 (pttt) cc_final: 0.7296 (pptt) REVERT: A 533 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5418 (mt) REVERT: A 684 MET cc_start: 0.3461 (ppp) cc_final: 0.3006 (ppp) REVERT: A 791 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7208 (mtmm) REVERT: A 824 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6276 (pp20) REVERT: A 836 PHE cc_start: 0.2744 (OUTLIER) cc_final: 0.1745 (p90) REVERT: A 837 MET cc_start: 0.1455 (mmp) cc_final: 0.0140 (mmp) REVERT: A 865 LEU cc_start: 0.6417 (mt) cc_final: 0.6058 (mp) outliers start: 46 outliers final: 24 residues processed: 176 average time/residue: 0.5734 time to fit residues: 109.4010 Evaluate side-chains 165 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR 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 476 SER Chi-restraints excluded: chain A residue 533 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 791 LYS Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1066 THR 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: 0.7980 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4805 r_free = 0.4805 target = 0.178921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.155615 restraints weight = 32926.225| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.17 r_work: 0.4333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12526 Z= 0.174 Angle : 0.828 14.338 17248 Z= 0.409 Chirality : 0.046 0.261 1993 Planarity : 0.006 0.062 1994 Dihedral : 14.983 77.157 2398 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.03 % Allowed : 34.34 % 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: -1.54 (0.22), residues: 1343 helix: 0.01 (0.21), residues: 581 sheet: -2.80 (0.50), residues: 91 loop : -1.69 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 789 TYR 0.027 0.002 TYR A1357 PHE 0.026 0.002 PHE A 894 TRP 0.049 0.004 TRP A 316 HIS 0.005 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00416 (12525) covalent geometry : angle 0.82814 (17246) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.62163 ( 2) hydrogen bonds : bond 0.04642 ( 515) hydrogen bonds : angle 5.23439 ( 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 173 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2448 (OUTLIER) cc_final: 0.1852 (mp) REVERT: A 349 ASP cc_start: 0.4124 (m-30) cc_final: 0.3696 (m-30) REVERT: A 390 TYR cc_start: 0.7107 (t80) cc_final: 0.6852 (m-80) REVERT: A 507 LYS cc_start: 0.7652 (pttt) cc_final: 0.7239 (pptt) REVERT: A 533 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5366 (mt) REVERT: A 791 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7250 (mtmm) REVERT: A 824 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: A 836 PHE cc_start: 0.2786 (OUTLIER) cc_final: 0.1825 (p90) REVERT: A 842 MET cc_start: 0.6838 (tpp) cc_final: 0.6254 (ttm) outliers start: 37 outliers final: 26 residues processed: 169 average time/residue: 0.5855 time to fit residues: 107.1279 Evaluate side-chains 162 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 187 ARG Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 THR 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 476 SER Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 533 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 791 LYS Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 853 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.178901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.155749 restraints weight = 32009.608| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.14 r_work: 0.4335 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12526 Z= 0.169 Angle : 0.824 14.021 17248 Z= 0.407 Chirality : 0.045 0.259 1993 Planarity : 0.006 0.061 1994 Dihedral : 15.001 77.048 2398 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.35 % Allowed : 33.93 % 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: -1.59 (0.22), residues: 1343 helix: -0.07 (0.21), residues: 586 sheet: -2.81 (0.50), residues: 91 loop : -1.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 789 TYR 0.026 0.002 TYR A1357 PHE 0.028 0.002 PHE A 498 TRP 0.049 0.003 TRP A 316 HIS 0.006 0.001 HIS A1041 Details of bonding type rmsd covalent geometry : bond 0.00404 (12525) covalent geometry : angle 0.82429 (17246) SS BOND : bond 0.00274 ( 1) SS BOND : angle 0.76062 ( 2) hydrogen bonds : bond 0.04673 ( 515) hydrogen bonds : angle 5.27117 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3979.17 seconds wall clock time: 68 minutes 44.86 seconds (4124.86 seconds total)