Starting phenix.real_space_refine on Wed Apr 30 09:07:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9p_40241/04_2025/8s9p_40241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9p_40241/04_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_40241/04_2025/8s9p_40241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9p_40241/04_2025/8s9p_40241.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9p_40241/04_2025/8s9p_40241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9p_40241/04_2025/8s9p_40241.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.05, per 1000 atoms: 0.65 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.57 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: 4.75 Time building geometry restraints manager: 3.13 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- 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 : 21.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (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 TRP 0.111 0.003 TRP B1186 HIS 0.009 0.001 HIS B 642 PHE 0.010 0.001 PHE B 598 TYR 0.036 0.002 TYR B 654 ARG 0.012 0.000 ARG A1982 Details of bonding type rmsd hydrogen bonds : bond 0.26797 ( 296) hydrogen bonds : angle 10.41186 ( 705) SS BOND : bond 0.00307 ( 11) SS BOND : angle 0.72401 ( 22) covalent geometry : bond 0.00478 ( 9506) covalent geometry : angle 0.82458 (12947) *********************** 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 : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 TRP cc_start: 0.7715 (m-10) cc_final: 0.7336 (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: 0.2150 time to fit residues: 58.0745 Evaluate side-chains 190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 B1109 ASN B1114 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084162 restraints weight = 21768.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087654 restraints weight = 11564.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090041 restraints weight = 7535.138| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9517 Z= 0.136 Angle : 0.688 10.153 12969 Z= 0.358 Chirality : 0.050 0.202 1440 Planarity : 0.005 0.059 1683 Dihedral : 5.890 45.052 1312 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.15 % Allowed : 28.16 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -0.87 (0.26), residues: 377 loop : -1.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1186 HIS 0.005 0.001 HIS A2048 PHE 0.018 0.001 PHE B 949 TYR 0.018 0.002 TYR B1068 ARG 0.007 0.001 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 296) hydrogen bonds : angle 7.38308 ( 705) SS BOND : bond 0.00288 ( 11) SS BOND : angle 0.67768 ( 22) covalent geometry : bond 0.00316 ( 9506) covalent geometry : angle 0.68840 (12947) *********************** 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 239 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7867 (ptt90) REVERT: A 1983 GLU cc_start: 0.8369 (pp20) cc_final: 0.8068 (pp20) REVERT: A 2036 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 548 LEU cc_start: 0.8910 (tt) cc_final: 0.8619 (tt) REVERT: B 683 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7971 (t80) REVERT: B 685 MET cc_start: 0.4841 (mpp) cc_final: 0.4557 (mmp) REVERT: B 687 ILE cc_start: 0.7160 (tp) cc_final: 0.6761 (pt) REVERT: B 688 HIS cc_start: 0.7275 (t-170) cc_final: 0.6701 (t-170) REVERT: B 834 ASP cc_start: 0.8149 (t0) cc_final: 0.7851 (t0) REVERT: B 998 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7249 (ttp80) REVERT: B 1099 ASP cc_start: 0.7571 (t0) cc_final: 0.7247 (t70) REVERT: B 1153 LEU cc_start: 0.8615 (mt) cc_final: 0.8208 (pp) REVERT: B 1181 MET cc_start: 0.8522 (tmm) cc_final: 0.8180 (tmm) REVERT: B 1197 MET cc_start: 0.8756 (mpp) cc_final: 0.8486 (mpp) REVERT: B 1216 LEU cc_start: 0.8306 (pt) cc_final: 0.7648 (tt) REVERT: C 36 THR cc_start: 0.8825 (m) cc_final: 0.8593 (p) REVERT: C 79 GLU cc_start: 0.8338 (mp0) cc_final: 0.7971 (mp0) REVERT: C 118 LYS cc_start: 0.8276 (mptt) cc_final: 0.7640 (pttt) outliers start: 42 outliers final: 17 residues processed: 223 average time/residue: 0.2234 time to fit residues: 69.2400 Evaluate side-chains 194 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1975 TRP 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 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 90 optimal weight: 4.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3725 r_free = 0.3725 target = 0.106103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078654 restraints weight = 22777.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081895 restraints weight = 12458.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084222 restraints weight = 8317.219| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9517 Z= 0.283 Angle : 0.747 8.519 12969 Z= 0.388 Chirality : 0.051 0.213 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.630 44.385 1292 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.16 % Favored : 89.75 % Rotamer: Outliers : 6.82 % Allowed : 26.28 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1181 helix: -4.54 (0.22), residues: 12 sheet: -1.17 (0.26), residues: 384 loop : -1.62 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B1186 HIS 0.005 0.001 HIS B 562 PHE 0.018 0.002 PHE B 746 TYR 0.022 0.002 TYR B1068 ARG 0.011 0.001 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 296) hydrogen bonds : angle 6.97992 ( 705) SS BOND : bond 0.00439 ( 11) SS BOND : angle 0.80781 ( 22) covalent geometry : bond 0.00637 ( 9506) covalent geometry : angle 0.74705 (12947) *********************** 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 242 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8298 (mtm110) cc_final: 0.7939 (ptt90) REVERT: A 1994 GLU cc_start: 0.8602 (tt0) cc_final: 0.8294 (tt0) REVERT: A 2036 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7440 (t80) REVERT: B 685 MET cc_start: 0.5222 (mpp) cc_final: 0.4963 (mmp) REVERT: B 687 ILE cc_start: 0.7391 (tp) cc_final: 0.6980 (pt) REVERT: B 773 ARG cc_start: 0.8236 (tpt170) cc_final: 0.7451 (mmm-85) REVERT: B 791 ASP cc_start: 0.8638 (m-30) cc_final: 0.8424 (m-30) REVERT: B 993 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: B 1099 ASP cc_start: 0.7745 (t0) cc_final: 0.7453 (t70) REVERT: B 1178 MET cc_start: 0.9589 (pmm) cc_final: 0.9230 (pmm) REVERT: B 1181 MET cc_start: 0.8500 (tmm) cc_final: 0.7921 (tmm) REVERT: B 1197 MET cc_start: 0.8875 (mpp) cc_final: 0.8437 (mpp) REVERT: B 1299 MET cc_start: 0.8125 (ptp) cc_final: 0.7754 (ptp) REVERT: B 1323 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7288 (mm) REVERT: C 79 GLU cc_start: 0.8553 (mp0) cc_final: 0.8020 (mp0) outliers start: 69 outliers final: 39 residues processed: 223 average time/residue: 0.2128 time to fit residues: 67.5547 Evaluate side-chains 207 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 1953 LEU 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 596 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 681 LEU 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 845 THR 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 986 LEU 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 1086 ILE Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1214 ASN 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 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 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 62 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.108477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081094 restraints weight = 22330.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084477 restraints weight = 12003.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086894 restraints weight = 7919.767| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9517 Z= 0.164 Angle : 0.692 9.523 12969 Z= 0.351 Chirality : 0.050 0.211 1440 Planarity : 0.005 0.060 1683 Dihedral : 5.428 45.293 1292 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 6.13 % Allowed : 27.67 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.04 (0.26), residues: 382 loop : -1.58 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 PHE 0.015 0.002 PHE B 483 TYR 0.018 0.002 TYR B1068 ARG 0.012 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 296) hydrogen bonds : angle 6.70896 ( 705) SS BOND : bond 0.00350 ( 11) SS BOND : angle 0.75315 ( 22) covalent geometry : bond 0.00377 ( 9506) covalent geometry : angle 0.69214 (12947) *********************** 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 242 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8352 (mtm110) cc_final: 0.7971 (ptt90) REVERT: A 1956 ASN cc_start: 0.7266 (t0) cc_final: 0.6885 (m-40) REVERT: A 1974 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7951 (mmp80) REVERT: A 2036 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 548 LEU cc_start: 0.8987 (tt) cc_final: 0.8756 (tt) REVERT: B 638 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7108 (pp30) REVERT: B 685 MET cc_start: 0.5207 (mpp) cc_final: 0.4887 (mmp) REVERT: B 834 ASP cc_start: 0.8446 (t0) cc_final: 0.8135 (m-30) REVERT: B 883 LYS cc_start: 0.8774 (pttm) cc_final: 0.8552 (pttm) REVERT: B 993 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7345 (t-90) REVERT: B 998 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.6924 (ttp80) REVERT: B 1056 ARG cc_start: 0.8449 (mmm160) cc_final: 0.8147 (mmt-90) REVERT: B 1178 MET cc_start: 0.9581 (pmm) cc_final: 0.9241 (pmm) REVERT: B 1181 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7755 (tmm) REVERT: B 1197 MET cc_start: 0.8830 (mpp) cc_final: 0.8189 (mpp) REVERT: B 1214 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.7003 (m110) REVERT: B 1316 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8658 (ttp80) REVERT: B 1323 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7236 (mm) REVERT: C 79 GLU cc_start: 0.8480 (mp0) cc_final: 0.7921 (mp0) outliers start: 62 outliers final: 37 residues processed: 220 average time/residue: 0.2004 time to fit residues: 62.7660 Evaluate side-chains 213 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 1919 SER Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL 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 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 603 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 732 SER 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 852 VAL 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 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 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1214 ASN Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1226 LEU 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 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B1271 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076733 restraints weight = 22893.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.079927 restraints weight = 12520.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082189 restraints weight = 8372.537| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 9517 Z= 0.337 Angle : 0.797 10.175 12969 Z= 0.411 Chirality : 0.053 0.241 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.947 47.598 1292 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.09 % Favored : 88.74 % Rotamer: Outliers : 8.60 % Allowed : 26.98 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.36 (0.25), residues: 400 loop : -1.72 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B1186 HIS 0.005 0.001 HIS B 562 PHE 0.018 0.002 PHE B 746 TYR 0.022 0.002 TYR B1068 ARG 0.005 0.001 ARG A1977 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 296) hydrogen bonds : angle 6.94294 ( 705) SS BOND : bond 0.00523 ( 11) SS BOND : angle 0.90929 ( 22) covalent geometry : bond 0.00757 ( 9506) covalent geometry : angle 0.79672 (12947) *********************** 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 264 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 177 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1994 GLU cc_start: 0.8665 (tt0) cc_final: 0.8321 (tt0) REVERT: A 2036 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7498 (t80) REVERT: B 493 LEU cc_start: 0.8740 (tp) cc_final: 0.8344 (tp) REVERT: B 687 ILE cc_start: 0.7574 (tp) cc_final: 0.6995 (pt) REVERT: B 773 ARG cc_start: 0.8328 (tpt170) cc_final: 0.7357 (mmm-85) REVERT: B 883 LYS cc_start: 0.8711 (pttm) cc_final: 0.8403 (pttm) REVERT: B 993 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7459 (t-90) REVERT: B 1056 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8350 (mmt-90) REVERT: B 1099 ASP cc_start: 0.7710 (t0) cc_final: 0.7278 (t0) REVERT: B 1181 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7749 (tmm) REVERT: B 1197 MET cc_start: 0.8926 (mpp) cc_final: 0.8240 (mpp) REVERT: B 1323 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7630 (mm) REVERT: C 79 GLU cc_start: 0.8597 (mp0) cc_final: 0.8136 (mp0) REVERT: C 110 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6662 (tp30) outliers start: 87 outliers final: 54 residues processed: 241 average time/residue: 0.2089 time to fit residues: 70.8933 Evaluate side-chains 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 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 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU 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 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL 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 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 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 1226 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1293 LEU 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 83 LEU Chi-restraints excluded: chain C residue 84 LEU 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 113 optimal weight: 0.0980 chunk 69 optimal weight: 0.0670 chunk 104 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN B 601 ASN B 638 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.109273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081739 restraints weight = 22353.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085193 restraints weight = 12052.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087621 restraints weight = 7962.705| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9517 Z= 0.132 Angle : 0.705 8.280 12969 Z= 0.354 Chirality : 0.050 0.214 1440 Planarity : 0.005 0.060 1683 Dihedral : 5.460 46.873 1292 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.24 % Allowed : 29.94 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -1.03 (0.25), residues: 386 loop : -1.52 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B1186 HIS 0.004 0.001 HIS A2048 PHE 0.014 0.001 PHE B 483 TYR 0.019 0.002 TYR B 654 ARG 0.015 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 296) hydrogen bonds : angle 6.65095 ( 705) SS BOND : bond 0.00305 ( 11) SS BOND : angle 0.76285 ( 22) covalent geometry : bond 0.00309 ( 9506) covalent geometry : angle 0.70468 (12947) *********************** 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 233 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1917 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 1956 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6465 (m-40) REVERT: A 2036 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 834 ASP cc_start: 0.8343 (t0) cc_final: 0.8091 (m-30) REVERT: B 883 LYS cc_start: 0.8774 (pttm) cc_final: 0.8394 (pttm) REVERT: B 993 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7386 (t-90) REVERT: B 998 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.6909 (ttp80) REVERT: B 1056 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8131 (mmt-90) REVERT: B 1181 MET cc_start: 0.8316 (tmm) cc_final: 0.7660 (tmm) REVERT: B 1197 MET cc_start: 0.8815 (mpp) cc_final: 0.8050 (mpp) REVERT: B 1316 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8604 (ttp80) REVERT: B 1323 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (mm) REVERT: C 79 GLU cc_start: 0.8410 (mp0) cc_final: 0.7954 (mp0) outliers start: 53 outliers final: 33 residues processed: 219 average time/residue: 0.2026 time to fit residues: 63.2393 Evaluate side-chains 204 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 1942 VAL Chi-restraints excluded: chain A residue 1956 ASN 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 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 787 VAL 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 1105 ILE 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 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN A2007 GLN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080087 restraints weight = 22592.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083467 restraints weight = 12118.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085845 restraints weight = 7984.581| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9517 Z= 0.200 Angle : 0.724 8.115 12969 Z= 0.364 Chirality : 0.050 0.204 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.530 48.228 1292 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.86 % Rotamer: Outliers : 6.32 % Allowed : 29.84 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.18 (0.25), residues: 393 loop : -1.61 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 PHE 0.013 0.002 PHE B 746 TYR 0.024 0.002 TYR B1175 ARG 0.008 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 296) hydrogen bonds : angle 6.60214 ( 705) SS BOND : bond 0.00380 ( 11) SS BOND : angle 0.78419 ( 22) covalent geometry : bond 0.00464 ( 9506) covalent geometry : angle 0.72367 (12947) *********************** 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 232 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1956 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6577 (m-40) REVERT: A 1994 GLU cc_start: 0.8604 (tt0) cc_final: 0.8391 (tt0) REVERT: A 2036 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7375 (t80) REVERT: B 493 LEU cc_start: 0.8670 (tp) cc_final: 0.8260 (tp) REVERT: B 773 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7192 (mmm-85) REVERT: B 834 ASP cc_start: 0.8405 (t0) cc_final: 0.8186 (m-30) REVERT: B 883 LYS cc_start: 0.8717 (pttm) cc_final: 0.8486 (pttm) REVERT: B 990 MET cc_start: 0.8898 (tpp) cc_final: 0.8636 (tpp) REVERT: B 993 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: B 998 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.6888 (ttp80) REVERT: B 1181 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7636 (tmm) REVERT: B 1197 MET cc_start: 0.8852 (mpp) cc_final: 0.7959 (mpp) REVERT: B 1323 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7488 (mm) REVERT: C 79 GLU cc_start: 0.8477 (mp0) cc_final: 0.7992 (mp0) outliers start: 64 outliers final: 47 residues processed: 213 average time/residue: 0.2114 time to fit residues: 63.9067 Evaluate side-chains 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 1919 SER Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL 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 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 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 813 THR 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 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 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 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 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.109974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082576 restraints weight = 22434.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086075 restraints weight = 11833.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.088532 restraints weight = 7737.096| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9517 Z= 0.134 Angle : 0.722 10.827 12969 Z= 0.357 Chirality : 0.050 0.235 1440 Planarity : 0.005 0.071 1683 Dihedral : 5.335 47.855 1292 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.14 % Allowed : 30.63 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -0.92 (0.26), residues: 379 loop : -1.59 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 PHE 0.012 0.001 PHE B 483 TYR 0.019 0.002 TYR B1175 ARG 0.020 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 296) hydrogen bonds : angle 6.46775 ( 705) SS BOND : bond 0.00354 ( 11) SS BOND : angle 1.13137 ( 22) covalent geometry : bond 0.00313 ( 9506) covalent geometry : angle 0.72116 (12947) *********************** 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 230 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1893 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 1956 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6537 (m-40) REVERT: A 1994 GLU cc_start: 0.8531 (tt0) cc_final: 0.8271 (tt0) REVERT: A 2036 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7389 (t80) REVERT: B 493 LEU cc_start: 0.8613 (tp) cc_final: 0.8221 (tp) REVERT: B 584 MET cc_start: 0.8370 (ptp) cc_final: 0.7847 (ptp) REVERT: B 883 LYS cc_start: 0.8759 (pttm) cc_final: 0.8433 (pttm) REVERT: B 993 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: B 998 ARG cc_start: 0.7721 (mmt-90) cc_final: 0.6902 (ttp80) REVERT: B 1181 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7599 (tmm) REVERT: B 1197 MET cc_start: 0.8804 (mpp) cc_final: 0.8029 (mpp) REVERT: B 1216 LEU cc_start: 0.8209 (pt) cc_final: 0.7359 (tt) REVERT: B 1316 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8617 (ttp80) REVERT: B 1323 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7418 (mm) REVERT: C 79 GLU cc_start: 0.8419 (mp0) cc_final: 0.7915 (mp0) outliers start: 52 outliers final: 41 residues processed: 216 average time/residue: 0.2036 time to fit residues: 62.4420 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 1919 SER Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1956 ASN Chi-restraints excluded: chain A residue 1979 VAL 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 724 CYS Chi-restraints excluded: chain B residue 752 ILE 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 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 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 1138 VAL 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 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 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.110749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082976 restraints weight = 22629.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086550 restraints weight = 12013.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089099 restraints weight = 7870.552| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9517 Z= 0.128 Angle : 0.739 12.013 12969 Z= 0.363 Chirality : 0.050 0.222 1440 Planarity : 0.005 0.070 1683 Dihedral : 5.248 47.253 1292 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.14 % Allowed : 31.92 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1181 helix: -4.66 (0.21), residues: 18 sheet: -0.87 (0.26), residues: 388 loop : -1.56 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP B1186 HIS 0.004 0.001 HIS B 642 PHE 0.016 0.001 PHE C 71 TYR 0.018 0.002 TYR B1068 ARG 0.014 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 296) hydrogen bonds : angle 6.34593 ( 705) SS BOND : bond 0.00300 ( 11) SS BOND : angle 0.86453 ( 22) covalent geometry : bond 0.00300 ( 9506) covalent geometry : angle 0.73914 (12947) *********************** 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 232 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1893 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 1956 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6643 (m-40) REVERT: A 2036 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7334 (t80) REVERT: B 584 MET cc_start: 0.8223 (ptp) cc_final: 0.7819 (ptp) REVERT: B 779 ASP cc_start: 0.7865 (m-30) cc_final: 0.7538 (t0) REVERT: B 867 GLU cc_start: 0.8157 (pp20) cc_final: 0.7896 (pp20) REVERT: B 883 LYS cc_start: 0.8731 (pttm) cc_final: 0.8396 (pttm) REVERT: B 990 MET cc_start: 0.8380 (tpp) cc_final: 0.8146 (tpp) REVERT: B 993 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: B 998 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.6879 (ttp80) REVERT: B 1099 ASP cc_start: 0.7796 (t0) cc_final: 0.7556 (t0) REVERT: B 1153 LEU cc_start: 0.8525 (mt) cc_final: 0.7584 (pp) REVERT: B 1175 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6135 (t80) REVERT: B 1181 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: B 1197 MET cc_start: 0.8786 (mpp) cc_final: 0.8041 (mpp) REVERT: B 1216 LEU cc_start: 0.8171 (pt) cc_final: 0.7414 (tt) REVERT: B 1316 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8642 (ttp80) REVERT: B 1323 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7357 (mm) REVERT: C 79 GLU cc_start: 0.8445 (mp0) cc_final: 0.7939 (mp0) outliers start: 52 outliers final: 42 residues processed: 217 average time/residue: 0.2055 time to fit residues: 64.2896 Evaluate side-chains 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 1919 SER Chi-restraints excluded: chain A residue 1942 VAL 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 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 752 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR 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 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 1101 THR Chi-restraints excluded: chain B residue 1105 ILE 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 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 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.111981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084136 restraints weight = 22703.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087726 restraints weight = 12158.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090288 restraints weight = 7997.101| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9517 Z= 0.124 Angle : 0.751 11.282 12969 Z= 0.366 Chirality : 0.050 0.216 1440 Planarity : 0.005 0.071 1683 Dihedral : 5.200 46.752 1292 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.84 % Allowed : 32.11 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 1181 helix: -4.82 (0.28), residues: 12 sheet: -0.84 (0.26), residues: 390 loop : -1.44 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP B1186 HIS 0.013 0.001 HIS B 642 PHE 0.011 0.001 PHE B 483 TYR 0.019 0.002 TYR B1068 ARG 0.013 0.000 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 296) hydrogen bonds : angle 6.30970 ( 705) SS BOND : bond 0.00259 ( 11) SS BOND : angle 0.74161 ( 22) covalent geometry : bond 0.00290 ( 9506) covalent geometry : angle 0.75064 (12947) ********************** 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 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1893 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 1956 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6625 (m-40) REVERT: A 2036 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 2042 ASP cc_start: 0.8050 (m-30) cc_final: 0.7746 (m-30) REVERT: B 564 MET cc_start: 0.8604 (mmm) cc_final: 0.8348 (mmm) REVERT: B 584 MET cc_start: 0.8060 (ptp) cc_final: 0.7743 (ptp) REVERT: B 779 ASP cc_start: 0.7820 (m-30) cc_final: 0.7431 (t0) REVERT: B 883 LYS cc_start: 0.8769 (pttm) cc_final: 0.8437 (pttm) REVERT: B 993 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6844 (t-90) REVERT: B 998 ARG cc_start: 0.7728 (mmt-90) cc_final: 0.6867 (ttp80) REVERT: B 1008 MET cc_start: 0.9121 (ptp) cc_final: 0.8877 (ptp) REVERT: B 1099 ASP cc_start: 0.7775 (t0) cc_final: 0.7557 (t0) REVERT: B 1157 MET cc_start: 0.7705 (ppp) cc_final: 0.7484 (ppp) REVERT: B 1170 ARG cc_start: 0.4984 (mmt180) cc_final: 0.4147 (mmt180) REVERT: B 1175 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6141 (t80) REVERT: B 1181 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7562 (tmm) REVERT: B 1197 MET cc_start: 0.8767 (mpp) cc_final: 0.8033 (mpp) REVERT: B 1216 LEU cc_start: 0.8138 (pt) cc_final: 0.7408 (tt) REVERT: B 1316 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8681 (ttp80) REVERT: B 1323 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7279 (mm) REVERT: C 79 GLU cc_start: 0.8430 (mp0) cc_final: 0.8120 (mp0) outliers start: 49 outliers final: 40 residues processed: 211 average time/residue: 0.2024 time to fit residues: 60.7048 Evaluate side-chains 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 1919 SER Chi-restraints excluded: chain A residue 1942 VAL 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 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 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 864 ILE 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 1051 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE 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 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 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.111508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084142 restraints weight = 22535.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087502 restraints weight = 12445.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089830 restraints weight = 8419.637| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9517 Z= 0.268 Angle : 0.804 12.128 12969 Z= 0.401 Chirality : 0.052 0.226 1440 Planarity : 0.006 0.078 1683 Dihedral : 5.681 48.253 1292 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.08 % Favored : 89.84 % Rotamer: Outliers : 5.63 % Allowed : 31.72 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1181 helix: -4.68 (0.21), residues: 18 sheet: -1.03 (0.25), residues: 400 loop : -1.62 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.003 TRP B1186 HIS 0.013 0.001 HIS B 642 PHE 0.017 0.002 PHE C 71 TYR 0.027 0.002 TYR B1175 ARG 0.013 0.001 ARG B1316 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 296) hydrogen bonds : angle 6.54336 ( 705) SS BOND : bond 0.00456 ( 11) SS BOND : angle 0.92707 ( 22) covalent geometry : bond 0.00610 ( 9506) covalent geometry : angle 0.80345 (12947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.33 seconds wall clock time: 66 minutes 30.60 seconds (3990.60 seconds total)