Starting phenix.real_space_refine on Sat Aug 23 03:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9p_40241/08_2025/8s9p_40241.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 52 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5830 2.51 5 N 1650 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9288 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1351 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 7199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7199 Classifications: {'peptide': 914} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 870} Chain: "C" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 91} Time building chain proxies: 1.76, per 1000 atoms: 0.19 Number of scatterers: 9288 At special positions: 0 Unit cell: (103.75, 109.56, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1762 8.00 N 1650 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1017 " distance=2.03 Simple disulfide: pdb=" SG CYS B1013 " - pdb=" SG CYS B1028 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1313 " - pdb=" SG CYS B1324 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1333 " distance=2.03 Simple disulfide: pdb=" SG CYS B1335 " - pdb=" SG CYS B1348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 112 " 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: 0.89 Conformation dependent library (CDL) restraints added in 291.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 26 sheets defined 2.5% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'B' and resid 702 through 709 removed outlier: 3.932A pdb=" N ASN B 705 " --> pdb=" O CYS B 702 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN B 706 " --> pdb=" O GLY B 703 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY B 707 " --> pdb=" O ASP B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1013 removed outlier: 4.791A pdb=" N GLU B1009 " --> pdb=" O CYS B1006 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN B1010 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B1012 " --> pdb=" O GLU B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1320 removed outlier: 3.621A pdb=" N GLY B1318 " --> pdb=" O SER B1315 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS B1320 " --> pdb=" O ASN B1317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1871 through 1874 removed outlier: 4.244A pdb=" N VAL A2043 " --> pdb=" O GLU A1917 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A1917 " --> pdb=" O VAL A2043 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A2045 " --> pdb=" O HIS A1915 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS A1915 " --> pdb=" O VAL A2045 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1871 through 1874 removed outlier: 4.716A pdb=" N VAL A2043 " --> pdb=" O LEU A2050 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1879 through 1882 removed outlier: 3.536A pdb=" N VAL A1879 " --> pdb=" O LEU A2016 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A2016 " --> pdb=" O VAL A1879 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A1944 " --> pdb=" O VAL A1929 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TRP A1931 " --> pdb=" O VAL A1942 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A1942 " --> pdb=" O TRP A1931 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 450 through 453 Processing sheet with id=AA5, first strand: chain 'B' and resid 470 through 476 removed outlier: 4.422A pdb=" N ALA B 472 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 494 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU B 504 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 515 through 519 removed outlier: 4.027A pdb=" N GLY B 515 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 527 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE B 535 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 562 removed outlier: 4.267A pdb=" N ALA B 558 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 579 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 603 through 606 removed outlier: 3.708A pdb=" N TRP B 614 " --> pdb=" O GLU B 623 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 622 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 643 through 649 removed outlier: 4.218A pdb=" N ALA B 645 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 656 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 712 through 716 Processing sheet with id=AB2, first strand: chain 'B' and resid 764 through 766 Processing sheet with id=AB3, first strand: chain 'B' and resid 775 through 781 removed outlier: 4.598A pdb=" N ALA B 777 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 797 " --> pdb=" O VAL B 810 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 821 through 824 removed outlier: 6.827A pdb=" N ILE B 840 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 861 through 867 removed outlier: 4.631A pdb=" N ASP B 863 " --> pdb=" O THR B 876 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 867 " --> pdb=" O TYR B 872 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 872 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE B 884 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 905 through 911 removed outlier: 6.853A pdb=" N ILE B 927 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 952 through 954 removed outlier: 6.569A pdb=" N ILE B 968 " --> pdb=" O LEU B 982 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1071 through 1073 removed outlier: 6.963A pdb=" N ILE B1052 " --> pdb=" O MET B1299 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET B1299 " --> pdb=" O ILE B1052 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA B1054 " --> pdb=" O MET B1297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1071 through 1073 Processing sheet with id=AC1, first strand: chain 'B' and resid 1086 through 1089 removed outlier: 6.693A pdb=" N ILE B1105 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1128 through 1131 removed outlier: 3.809A pdb=" N GLY B1128 " --> pdb=" O THR B1141 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B1148 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1173 through 1175 removed outlier: 6.902A pdb=" N LEU B1192 " --> pdb=" O LEU B1205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1215 through 1219 removed outlier: 7.177A pdb=" N ILE B1235 " --> pdb=" O LEU B1248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1259 through 1261 removed outlier: 3.786A pdb=" N TRP B1267 " --> pdb=" O HIS B1276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1323 through 1327 Processing sheet with id=AC7, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.672A pdb=" N VAL C 37 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 116 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 111 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C 99 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 113 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 97 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.596A pdb=" N LEU C 83 " --> pdb=" O ARG C 78 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.15 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: 3138 1.34 - 1.46: 2137 1.46 - 1.58: 4160 1.58 - 1.70: 2 1.70 - 1.82: 69 Bond restraints: 9506 Sorted by residual: bond pdb=" CB PRO B 684 " pdb=" CG PRO B 684 " ideal model delta sigma weight residual 1.492 1.689 -0.197 5.00e-02 4.00e+02 1.55e+01 bond pdb=" CB PRO B 455 " pdb=" CG PRO B 455 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.22e+00 bond pdb=" CA ASP B 859 " pdb=" CB ASP B 859 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.27e-02 6.20e+03 3.11e+00 bond pdb=" CG1 ILE A1894 " pdb=" CD1 ILE A1894 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CB ASP B1185 " pdb=" CG ASP B1185 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.27e+00 ... (remaining 9501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 12863 3.67 - 7.33: 73 7.33 - 11.00: 9 11.00 - 14.66: 1 14.66 - 18.33: 1 Bond angle restraints: 12947 Sorted by residual: angle pdb=" CA PRO B 684 " pdb=" N PRO B 684 " pdb=" CD PRO B 684 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.29e+01 angle pdb=" CB MET B1157 " pdb=" CG MET B1157 " pdb=" SD MET B1157 " ideal model delta sigma weight residual 112.70 131.03 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" CA MET B1157 " pdb=" CB MET B1157 " pdb=" CG MET B1157 " ideal model delta sigma weight residual 114.10 124.39 -10.29 2.00e+00 2.50e-01 2.65e+01 angle pdb=" CA GLU B 760 " pdb=" CB GLU B 760 " pdb=" CG GLU B 760 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA PRO B 455 " pdb=" N PRO B 455 " pdb=" CD PRO B 455 " ideal model delta sigma weight residual 112.00 105.91 6.09 1.40e+00 5.10e-01 1.89e+01 ... (remaining 12942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4795 17.97 - 35.93: 674 35.93 - 53.90: 154 53.90 - 71.86: 27 71.86 - 89.83: 10 Dihedral angle restraints: 5660 sinusoidal: 2261 harmonic: 3399 Sorted by residual: dihedral pdb=" CB CYS C 98 " pdb=" SG CYS C 98 " pdb=" SG CYS C 112 " pdb=" CB CYS C 112 " ideal model delta sinusoidal sigma weight residual 93.00 37.28 55.72 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS B 702 " pdb=" SG CYS B 702 " pdb=" SG CYS B 713 " pdb=" CB CYS B 713 " ideal model delta sinusoidal sigma weight residual -86.00 -123.25 37.25 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA THR A2006 " pdb=" C THR A2006 " pdb=" N GLN A2007 " pdb=" CA GLN A2007 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 969 0.043 - 0.086: 319 0.086 - 0.128: 131 0.128 - 0.171: 17 0.171 - 0.214: 4 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB ILE B 884 " pdb=" CA ILE B 884 " pdb=" CG1 ILE B 884 " pdb=" CG2 ILE B 884 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN B 988 " pdb=" N ASN B 988 " pdb=" C ASN B 988 " pdb=" CB ASN B 988 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B 927 " pdb=" CA ILE B 927 " pdb=" CG1 ILE B 927 " pdb=" CG2 ILE B 927 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1437 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1186 " 0.043 2.00e-02 2.50e+03 4.16e-02 4.33e+01 pdb=" CG TRP B1186 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP B1186 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP B1186 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B1186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1186 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1186 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1186 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1186 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B1186 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 683 " 0.070 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO B 684 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 684 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 684 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 859 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" CG ASP B 859 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASP B 859 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP B 859 " 0.023 2.00e-02 2.50e+03 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 182 2.60 - 3.17: 8287 3.17 - 3.75: 15317 3.75 - 4.32: 20023 4.32 - 4.90: 32863 Nonbonded interactions: 76672 Sorted by model distance: nonbonded pdb=" NH1 ARG C 74 " pdb=" OE1 GLU C 90 " model vdw 2.024 3.120 nonbonded pdb=" OD2 ASP B 911 " pdb=" OG SER B 914 " model vdw 2.108 3.040 nonbonded pdb=" NH1 ARG B 749 " pdb=" OG SER B 774 " model vdw 2.140 3.120 nonbonded pdb=" OH TYR B 613 " pdb=" NZ LYS B 668 " model vdw 2.187 3.120 nonbonded pdb=" N GLU B 623 " pdb=" OE1 GLU B 623 " model vdw 2.208 3.120 ... (remaining 76667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.197 9517 Z= 0.195 Angle : 0.824 18.326 12969 Z= 0.434 Chirality : 0.050 0.214 1440 Planarity : 0.006 0.098 1683 Dihedral : 17.164 89.831 3443 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.31 % Favored : 90.52 % Rotamer: Outliers : 1.88 % Allowed : 33.60 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.07 (0.24), residues: 1181 helix: -3.92 (0.76), residues: 18 sheet: -1.24 (0.26), residues: 391 loop : -1.40 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1982 TYR 0.036 0.002 TYR B 654 PHE 0.010 0.001 PHE B 598 TRP 0.111 0.003 TRP B1186 HIS 0.009 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9506) covalent geometry : angle 0.82458 (12947) SS BOND : bond 0.00307 ( 11) SS BOND : angle 0.72401 ( 22) hydrogen bonds : bond 0.26797 ( 296) hydrogen bonds : angle 10.41186 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 TRP cc_start: 0.7715 (m-10) cc_final: 0.7320 (m-10) REVERT: B 1099 ASP cc_start: 0.7315 (t0) cc_final: 0.6837 (p0) outliers start: 19 outliers final: 12 residues processed: 195 average time/residue: 0.0741 time to fit residues: 20.4662 Evaluate side-chains 189 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1214 ASN Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.0470 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN B 496 ASN B 601 ASN B 638 GLN B 664 ASN B1109 ASN B1114 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.106248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079102 restraints weight = 22671.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082372 restraints weight = 12235.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084662 restraints weight = 8096.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086275 restraints weight = 6080.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087314 restraints weight = 4966.439| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9517 Z= 0.261 Angle : 0.747 9.575 12969 Z= 0.393 Chirality : 0.052 0.223 1440 Planarity : 0.006 0.064 1683 Dihedral : 6.363 51.741 1312 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.31 % Favored : 90.60 % Rotamer: Outliers : 6.92 % Allowed : 26.28 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.16 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.15 (0.26), residues: 372 loop : -1.59 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 74 TYR 0.023 0.002 TYR B1068 PHE 0.023 0.002 PHE B 949 TRP 0.036 0.002 TRP B1186 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 9506) covalent geometry : angle 0.74700 (12947) SS BOND : bond 0.00429 ( 11) SS BOND : angle 0.79254 ( 22) hydrogen bonds : bond 0.04106 ( 296) hydrogen bonds : angle 7.36026 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7833 (ptt90) REVERT: A 2036 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 449 ASP cc_start: 0.7501 (m-30) cc_final: 0.7098 (m-30) REVERT: B 685 MET cc_start: 0.5182 (mpp) cc_final: 0.4801 (mmp) REVERT: B 687 ILE cc_start: 0.7278 (tp) cc_final: 0.6956 (pt) REVERT: B 773 ARG cc_start: 0.8144 (tpt170) cc_final: 0.7398 (mmm-85) REVERT: B 1099 ASP cc_start: 0.7635 (t0) cc_final: 0.7342 (t70) REVERT: B 1181 MET cc_start: 0.8603 (tmm) cc_final: 0.8209 (tmm) REVERT: B 1197 MET cc_start: 0.8800 (mpp) cc_final: 0.8523 (mpp) REVERT: B 1323 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7259 (mm) REVERT: C 79 GLU cc_start: 0.8480 (mp0) cc_final: 0.8124 (mp0) REVERT: C 118 LYS cc_start: 0.8172 (mptt) cc_final: 0.7716 (pttt) outliers start: 70 outliers final: 42 residues processed: 229 average time/residue: 0.0779 time to fit residues: 24.8866 Evaluate side-chains 208 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain A residue 2050 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 664 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1129 LEU Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079328 restraints weight = 22575.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082655 restraints weight = 12121.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084970 restraints weight = 7986.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086608 restraints weight = 5981.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087679 restraints weight = 4877.864| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9517 Z= 0.220 Angle : 0.704 8.345 12969 Z= 0.366 Chirality : 0.050 0.217 1440 Planarity : 0.005 0.062 1683 Dihedral : 5.900 48.949 1297 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.98 % Favored : 90.94 % Rotamer: Outliers : 7.51 % Allowed : 26.38 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.17 (0.24), residues: 1181 helix: -4.54 (0.22), residues: 12 sheet: -1.10 (0.25), residues: 387 loop : -1.63 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1316 TYR 0.019 0.002 TYR B1068 PHE 0.016 0.002 PHE B 483 TRP 0.046 0.002 TRP B1186 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9506) covalent geometry : angle 0.70361 (12947) SS BOND : bond 0.00395 ( 11) SS BOND : angle 0.80466 ( 22) hydrogen bonds : bond 0.03634 ( 296) hydrogen bonds : angle 6.97784 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2036 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 449 ASP cc_start: 0.7411 (m-30) cc_final: 0.6824 (m-30) REVERT: B 883 LYS cc_start: 0.8730 (pttm) cc_final: 0.8443 (pttm) REVERT: B 993 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7287 (t-90) REVERT: B 998 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.6952 (ttp80) REVERT: B 1099 ASP cc_start: 0.7689 (t0) cc_final: 0.7367 (t70) REVERT: B 1178 MET cc_start: 0.9609 (pmm) cc_final: 0.9279 (pmm) REVERT: B 1181 MET cc_start: 0.8480 (tmm) cc_final: 0.7904 (tmm) REVERT: B 1197 MET cc_start: 0.8883 (mpp) cc_final: 0.8466 (mpp) REVERT: B 1323 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7396 (mm) REVERT: C 79 GLU cc_start: 0.8510 (mp0) cc_final: 0.7980 (mp0) REVERT: C 118 LYS cc_start: 0.8040 (mptt) cc_final: 0.7758 (tmtt) outliers start: 76 outliers final: 49 residues processed: 231 average time/residue: 0.0724 time to fit residues: 23.7079 Evaluate side-chains 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1129 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN B 638 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.078314 restraints weight = 23050.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081631 restraints weight = 12349.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083943 restraints weight = 8158.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085563 restraints weight = 6114.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086666 restraints weight = 5005.169| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9517 Z= 0.245 Angle : 0.736 8.364 12969 Z= 0.378 Chirality : 0.051 0.221 1440 Planarity : 0.005 0.063 1683 Dihedral : 5.981 47.859 1296 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.86 % Rotamer: Outliers : 8.60 % Allowed : 26.48 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.30 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.25 (0.24), residues: 405 loop : -1.68 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1316 TYR 0.019 0.002 TYR B1068 PHE 0.016 0.002 PHE B 483 TRP 0.048 0.002 TRP B1186 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 9506) covalent geometry : angle 0.73606 (12947) SS BOND : bond 0.00439 ( 11) SS BOND : angle 0.87843 ( 22) hydrogen bonds : bond 0.03456 ( 296) hydrogen bonds : angle 6.86850 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 176 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2036 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 638 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (pp30) REVERT: B 687 ILE cc_start: 0.7514 (tp) cc_final: 0.7027 (pt) REVERT: B 867 GLU cc_start: 0.8101 (pm20) cc_final: 0.7581 (pm20) REVERT: B 883 LYS cc_start: 0.8697 (pttm) cc_final: 0.8343 (pttm) REVERT: B 993 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7338 (t-90) REVERT: B 1099 ASP cc_start: 0.7655 (t0) cc_final: 0.7170 (t0) REVERT: B 1178 MET cc_start: 0.9625 (pmm) cc_final: 0.9272 (pmm) REVERT: B 1181 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: B 1197 MET cc_start: 0.8888 (mpp) cc_final: 0.8313 (mpp) REVERT: B 1323 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7636 (mm) REVERT: C 43 GLU cc_start: 0.7788 (mp0) cc_final: 0.7543 (pm20) REVERT: C 79 GLU cc_start: 0.8524 (mp0) cc_final: 0.8011 (mp0) REVERT: C 119 MET cc_start: 0.8160 (mpp) cc_final: 0.7665 (mpp) outliers start: 87 outliers final: 58 residues processed: 236 average time/residue: 0.0675 time to fit residues: 22.7954 Evaluate side-chains 226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1956 ASN A1984 GLN A1990 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077163 restraints weight = 23146.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080507 restraints weight = 12438.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082870 restraints weight = 8242.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084516 restraints weight = 6198.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085508 restraints weight = 5069.930| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 9517 Z= 0.267 Angle : 0.744 9.923 12969 Z= 0.385 Chirality : 0.052 0.233 1440 Planarity : 0.005 0.063 1683 Dihedral : 6.093 47.393 1296 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.25 % Favored : 89.67 % Rotamer: Outliers : 9.19 % Allowed : 27.37 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.37 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.35 (0.24), residues: 410 loop : -1.70 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1316 TYR 0.020 0.002 TYR B1068 PHE 0.024 0.002 PHE B 683 TRP 0.046 0.002 TRP B1186 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9506) covalent geometry : angle 0.74413 (12947) SS BOND : bond 0.00465 ( 11) SS BOND : angle 0.89182 ( 22) hydrogen bonds : bond 0.03471 ( 296) hydrogen bonds : angle 6.85597 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 170 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2036 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 552 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8472 (p0) REVERT: B 683 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8255 (t80) REVERT: B 685 MET cc_start: 0.5408 (mmp) cc_final: 0.4776 (mmp) REVERT: B 687 ILE cc_start: 0.7567 (tp) cc_final: 0.7079 (pt) REVERT: B 758 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7015 (t0) REVERT: B 773 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7164 (mmm-85) REVERT: B 867 GLU cc_start: 0.8083 (pm20) cc_final: 0.7555 (pm20) REVERT: B 883 LYS cc_start: 0.8680 (pttm) cc_final: 0.8453 (pttm) REVERT: B 993 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7314 (t-90) REVERT: B 1056 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8269 (mmt-90) REVERT: B 1099 ASP cc_start: 0.7651 (t0) cc_final: 0.7134 (t0) REVERT: B 1181 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7714 (tmm) REVERT: B 1197 MET cc_start: 0.8903 (mpp) cc_final: 0.8192 (mpp) REVERT: B 1316 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8612 (ttp80) REVERT: B 1323 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7581 (mm) REVERT: C 79 GLU cc_start: 0.8519 (mp0) cc_final: 0.8102 (mp0) REVERT: C 110 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6652 (tp30) outliers start: 93 outliers final: 61 residues processed: 241 average time/residue: 0.0709 time to fit residues: 24.5786 Evaluate side-chains 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 773 ARG Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN B 638 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081375 restraints weight = 22360.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084821 restraints weight = 11805.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087236 restraints weight = 7710.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088912 restraints weight = 5728.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090076 restraints weight = 4654.364| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9517 Z= 0.144 Angle : 0.694 8.361 12969 Z= 0.352 Chirality : 0.050 0.223 1440 Planarity : 0.005 0.062 1683 Dihedral : 5.735 46.515 1296 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.63 % Allowed : 31.03 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.16 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.09 (0.25), residues: 399 loop : -1.63 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1316 TYR 0.020 0.002 TYR B 654 PHE 0.016 0.002 PHE B 483 TRP 0.061 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9506) covalent geometry : angle 0.69365 (12947) SS BOND : bond 0.00392 ( 11) SS BOND : angle 0.99472 ( 22) hydrogen bonds : bond 0.02934 ( 296) hydrogen bonds : angle 6.59998 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1956 ASN cc_start: 0.6984 (OUTLIER) cc_final: 0.6527 (m-40) REVERT: A 2036 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7405 (t80) REVERT: B 584 MET cc_start: 0.8572 (ptm) cc_final: 0.8353 (ptp) REVERT: B 683 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 834 ASP cc_start: 0.8336 (t0) cc_final: 0.8063 (m-30) REVERT: B 883 LYS cc_start: 0.8747 (pttm) cc_final: 0.8487 (pttm) REVERT: B 993 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: B 998 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.6916 (ttp80) REVERT: B 1056 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8094 (mmt-90) REVERT: B 1181 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: B 1197 MET cc_start: 0.8825 (mpp) cc_final: 0.8012 (mpp) REVERT: B 1323 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7557 (mm) REVERT: C 79 GLU cc_start: 0.8414 (mp0) cc_final: 0.7955 (mp0) outliers start: 57 outliers final: 40 residues processed: 222 average time/residue: 0.0711 time to fit residues: 22.3169 Evaluate side-chains 206 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079963 restraints weight = 22466.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083327 restraints weight = 11974.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085719 restraints weight = 7889.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087360 restraints weight = 5895.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088555 restraints weight = 4798.166| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9517 Z= 0.187 Angle : 0.721 10.103 12969 Z= 0.366 Chirality : 0.050 0.247 1440 Planarity : 0.005 0.072 1683 Dihedral : 5.707 46.438 1294 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 7.11 % Allowed : 30.63 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.23 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.27 (0.24), residues: 415 loop : -1.59 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1316 TYR 0.018 0.002 TYR B 654 PHE 0.015 0.001 PHE B 483 TRP 0.065 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9506) covalent geometry : angle 0.72027 (12947) SS BOND : bond 0.00391 ( 11) SS BOND : angle 0.88393 ( 22) hydrogen bonds : bond 0.03051 ( 296) hydrogen bonds : angle 6.51806 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8354 (mtm110) cc_final: 0.8096 (mtm110) REVERT: A 1956 ASN cc_start: 0.6985 (OUTLIER) cc_final: 0.6607 (m-40) REVERT: A 2036 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 687 ILE cc_start: 0.7423 (tp) cc_final: 0.6944 (pt) REVERT: B 773 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7025 (mmm-85) REVERT: B 834 ASP cc_start: 0.8425 (t0) cc_final: 0.8138 (m-30) REVERT: B 883 LYS cc_start: 0.8720 (pttm) cc_final: 0.8198 (pttm) REVERT: B 990 MET cc_start: 0.8897 (tpp) cc_final: 0.8650 (tpp) REVERT: B 993 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: B 1056 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8189 (mmt-90) REVERT: B 1181 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: B 1197 MET cc_start: 0.8881 (mpp) cc_final: 0.8034 (mpp) REVERT: B 1316 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8608 (ttp80) REVERT: B 1323 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7564 (mm) REVERT: C 79 GLU cc_start: 0.8436 (mp0) cc_final: 0.7987 (mp0) outliers start: 72 outliers final: 53 residues processed: 221 average time/residue: 0.0682 time to fit residues: 21.3613 Evaluate side-chains 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1988 SER Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 773 ARG Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.080722 restraints weight = 22211.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084065 restraints weight = 11903.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086451 restraints weight = 7853.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088102 restraints weight = 5870.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089155 restraints weight = 4795.794| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9517 Z= 0.172 Angle : 0.728 10.228 12969 Z= 0.367 Chirality : 0.050 0.252 1440 Planarity : 0.005 0.080 1683 Dihedral : 5.658 45.930 1294 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 6.92 % Allowed : 31.03 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.15 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.14 (0.24), residues: 417 loop : -1.59 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1316 TYR 0.019 0.002 TYR B1068 PHE 0.017 0.001 PHE B 483 TRP 0.078 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9506) covalent geometry : angle 0.72736 (12947) SS BOND : bond 0.00377 ( 11) SS BOND : angle 0.85518 ( 22) hydrogen bonds : bond 0.02965 ( 296) hydrogen bonds : angle 6.49621 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 169 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8381 (mtm110) cc_final: 0.8118 (mtm110) REVERT: A 1952 GLN cc_start: 0.7477 (mt0) cc_final: 0.7178 (mp10) REVERT: A 1956 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6620 (m-40) REVERT: A 2036 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 493 LEU cc_start: 0.8525 (tp) cc_final: 0.8245 (tp) REVERT: B 584 MET cc_start: 0.8239 (ptp) cc_final: 0.7785 (ptp) REVERT: B 688 HIS cc_start: 0.7402 (t-170) cc_final: 0.6880 (t-170) REVERT: B 834 ASP cc_start: 0.8403 (t0) cc_final: 0.8085 (m-30) REVERT: B 883 LYS cc_start: 0.8749 (pttm) cc_final: 0.8222 (pttm) REVERT: B 990 MET cc_start: 0.8747 (tpp) cc_final: 0.8529 (tpp) REVERT: B 993 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7181 (t-90) REVERT: B 1175 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6284 (t80) REVERT: B 1181 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7664 (tmm) REVERT: B 1197 MET cc_start: 0.8891 (mpp) cc_final: 0.7950 (mpp) REVERT: B 1316 ARG cc_start: 0.8905 (ttp80) cc_final: 0.8649 (ttp80) REVERT: B 1323 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7522 (mm) REVERT: C 79 GLU cc_start: 0.8431 (mp0) cc_final: 0.7981 (mp0) outliers start: 70 outliers final: 58 residues processed: 219 average time/residue: 0.0589 time to fit residues: 18.9775 Evaluate side-chains 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1988 SER Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1268 THR Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.110731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083618 restraints weight = 21947.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087115 restraints weight = 11562.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089581 restraints weight = 7531.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091272 restraints weight = 5586.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092454 restraints weight = 4532.093| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9517 Z= 0.132 Angle : 0.731 10.760 12969 Z= 0.365 Chirality : 0.050 0.235 1440 Planarity : 0.005 0.075 1683 Dihedral : 5.501 45.046 1294 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.63 % Allowed : 32.61 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.05 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.02 (0.24), residues: 416 loop : -1.54 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1316 TYR 0.018 0.002 TYR B1068 PHE 0.016 0.001 PHE C 71 TRP 0.068 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9506) covalent geometry : angle 0.73044 (12947) SS BOND : bond 0.00313 ( 11) SS BOND : angle 0.77543 ( 22) hydrogen bonds : bond 0.02854 ( 296) hydrogen bonds : angle 6.41892 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8188 (mtm110) REVERT: A 1956 ASN cc_start: 0.6985 (OUTLIER) cc_final: 0.6665 (m-40) REVERT: A 2036 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7325 (t80) REVERT: B 493 LEU cc_start: 0.8502 (tp) cc_final: 0.8211 (tp) REVERT: B 584 MET cc_start: 0.8008 (ptp) cc_final: 0.7607 (ptp) REVERT: B 688 HIS cc_start: 0.7377 (t-170) cc_final: 0.6759 (t-170) REVERT: B 834 ASP cc_start: 0.8290 (t0) cc_final: 0.8081 (m-30) REVERT: B 883 LYS cc_start: 0.8744 (pttm) cc_final: 0.8290 (pttm) REVERT: B 993 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7067 (t-90) REVERT: B 998 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7123 (ttp80) REVERT: B 1175 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 1181 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7599 (tmm) REVERT: B 1197 MET cc_start: 0.8846 (mpp) cc_final: 0.7911 (mpp) REVERT: B 1216 LEU cc_start: 0.8217 (pt) cc_final: 0.7354 (tt) REVERT: B 1316 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8637 (ttp80) REVERT: B 1323 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7480 (mm) REVERT: C 79 GLU cc_start: 0.8405 (mp0) cc_final: 0.7970 (mp0) outliers start: 57 outliers final: 44 residues processed: 222 average time/residue: 0.0933 time to fit residues: 29.4644 Evaluate side-chains 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.110645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083578 restraints weight = 22115.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087061 restraints weight = 11641.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.089477 restraints weight = 7578.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091245 restraints weight = 5625.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092291 restraints weight = 4549.563| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9517 Z= 0.129 Angle : 0.751 12.965 12969 Z= 0.369 Chirality : 0.050 0.237 1440 Planarity : 0.005 0.077 1683 Dihedral : 5.423 44.932 1294 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.24 % Allowed : 33.89 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.06 (0.24), residues: 1181 helix: -4.66 (0.21), residues: 18 sheet: -0.99 (0.25), residues: 417 loop : -1.54 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1316 TYR 0.019 0.002 TYR B 918 PHE 0.011 0.001 PHE B 483 TRP 0.070 0.002 TRP B1186 HIS 0.006 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9506) covalent geometry : angle 0.75137 (12947) SS BOND : bond 0.00291 ( 11) SS BOND : angle 0.72585 ( 22) hydrogen bonds : bond 0.02814 ( 296) hydrogen bonds : angle 6.30912 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8215 (mtm110) REVERT: A 1956 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6657 (m-40) REVERT: A 1965 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6931 (mtp-110) REVERT: A 2036 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 493 LEU cc_start: 0.8515 (tp) cc_final: 0.8231 (tp) REVERT: B 584 MET cc_start: 0.7873 (ptp) cc_final: 0.7511 (ptp) REVERT: B 688 HIS cc_start: 0.7405 (t-170) cc_final: 0.6753 (t-170) REVERT: B 779 ASP cc_start: 0.7810 (m-30) cc_final: 0.7406 (t0) REVERT: B 883 LYS cc_start: 0.8756 (pttm) cc_final: 0.8375 (pttm) REVERT: B 990 MET cc_start: 0.7993 (tpp) cc_final: 0.7775 (tpp) REVERT: B 993 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6801 (t-90) REVERT: B 998 ARG cc_start: 0.7790 (mmt180) cc_final: 0.7043 (ttp80) REVERT: B 1099 ASP cc_start: 0.7752 (t0) cc_final: 0.6560 (t0) REVERT: B 1175 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 1181 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7617 (tmm) REVERT: B 1189 ASN cc_start: 0.7920 (p0) cc_final: 0.7609 (p0) REVERT: B 1197 MET cc_start: 0.8825 (mpp) cc_final: 0.7964 (mpp) REVERT: B 1216 LEU cc_start: 0.8260 (pt) cc_final: 0.7403 (tt) REVERT: B 1323 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7484 (mm) REVERT: C 35 GLU cc_start: 0.8783 (pm20) cc_final: 0.8377 (pt0) REVERT: C 79 GLU cc_start: 0.8397 (mp0) cc_final: 0.8112 (mp0) outliers start: 53 outliers final: 44 residues processed: 213 average time/residue: 0.0990 time to fit residues: 29.8098 Evaluate side-chains 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 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 = 0.3736 r_free = 0.3736 target = 0.106971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079919 restraints weight = 22478.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083245 restraints weight = 11974.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085596 restraints weight = 7872.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087187 restraints weight = 5885.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088330 restraints weight = 4799.105| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9517 Z= 0.238 Angle : 0.780 11.959 12969 Z= 0.393 Chirality : 0.051 0.256 1440 Planarity : 0.006 0.094 1683 Dihedral : 5.740 46.917 1294 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.48 % Favored : 90.43 % Rotamer: Outliers : 5.73 % Allowed : 33.10 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.18 (0.24), residues: 1181 helix: -4.68 (0.21), residues: 18 sheet: -1.19 (0.24), residues: 429 loop : -1.55 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B1316 TYR 0.019 0.002 TYR B1068 PHE 0.016 0.002 PHE C 71 TRP 0.074 0.002 TRP B1186 HIS 0.004 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9506) covalent geometry : angle 0.78016 (12947) SS BOND : bond 0.00429 ( 11) SS BOND : angle 0.82233 ( 22) hydrogen bonds : bond 0.03221 ( 296) hydrogen bonds : angle 6.49783 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1559.78 seconds wall clock time: 27 minutes 39.89 seconds (1659.89 seconds total)