Starting phenix.real_space_refine on Thu Feb 13 21:00:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9p_40241/02_2025/8s9p_40241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9p_40241/02_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_40241/02_2025/8s9p_40241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9p_40241/02_2025/8s9p_40241.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9p_40241/02_2025/8s9p_40241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9p_40241/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.17, per 1000 atoms: 0.56 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 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: 1.42 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: 4.53 Time building geometry restraints manager: 2.76 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: 0.650 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 9506 Z= 0.322 Angle : 0.825 18.326 12947 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 *********************** 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 : 1.092 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: 0.2333 time to fit residues: 63.1145 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 : 1.012 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084161 restraints weight = 21768.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087624 restraints weight = 11564.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090077 restraints weight = 7532.842| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 9506 Z= 0.212 Angle : 0.688 10.153 12947 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 *********************** 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 : 1.483 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: 0.8156 (mtm110) cc_final: 0.7864 (ptt90) REVERT: A 1983 GLU cc_start: 0.8366 (pp20) cc_final: 0.8066 (pp20) REVERT: A 2036 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 548 LEU cc_start: 0.8912 (tt) cc_final: 0.8622 (tt) REVERT: B 683 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 685 MET cc_start: 0.4833 (mpp) cc_final: 0.4550 (mmp) REVERT: B 687 ILE cc_start: 0.7163 (tp) cc_final: 0.6763 (pt) REVERT: B 688 HIS cc_start: 0.7276 (t-170) cc_final: 0.6703 (t-170) REVERT: B 834 ASP cc_start: 0.8147 (t0) cc_final: 0.7850 (t0) REVERT: B 998 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7249 (ttp80) REVERT: B 1099 ASP cc_start: 0.7559 (t0) cc_final: 0.7244 (t70) REVERT: B 1153 LEU cc_start: 0.8614 (mt) cc_final: 0.8203 (pp) REVERT: B 1181 MET cc_start: 0.8523 (tmm) cc_final: 0.8183 (tmm) REVERT: B 1197 MET cc_start: 0.8755 (mpp) cc_final: 0.8484 (mpp) REVERT: B 1216 LEU cc_start: 0.8306 (pt) cc_final: 0.7647 (tt) REVERT: C 36 THR cc_start: 0.8826 (m) cc_final: 0.8595 (p) REVERT: C 79 GLU cc_start: 0.8336 (mp0) cc_final: 0.7967 (mp0) REVERT: C 118 LYS cc_start: 0.8275 (mptt) cc_final: 0.7643 (pttt) outliers start: 42 outliers final: 17 residues processed: 223 average time/residue: 0.2287 time to fit residues: 71.2969 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 : 1.132 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079538 restraints weight = 22574.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082794 restraints weight = 12257.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085143 restraints weight = 8162.825| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9506 Z= 0.372 Angle : 0.720 8.378 12947 Z= 0.373 Chirality : 0.050 0.208 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.517 43.817 1292 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 6.32 % Allowed : 26.68 % Favored : 67.00 % 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: -2.14 (0.24), residues: 1181 helix: -4.54 (0.22), residues: 12 sheet: -1.10 (0.26), residues: 384 loop : -1.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B1186 HIS 0.004 0.001 HIS B 562 PHE 0.018 0.002 PHE B 746 TYR 0.021 0.002 TYR B1068 ARG 0.010 0.001 ARG B1316 *********************** 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: 64 poor density : 178 time to evaluate : 1.087 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: 0.8284 (mtm110) cc_final: 0.7922 (ptt90) REVERT: A 2036 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7422 (t80) REVERT: B 685 MET cc_start: 0.5117 (mpp) cc_final: 0.4858 (mmp) REVERT: B 687 ILE cc_start: 0.7335 (tp) cc_final: 0.6928 (pt) REVERT: B 773 ARG cc_start: 0.8164 (tpt170) cc_final: 0.7429 (mmm-85) REVERT: B 791 ASP cc_start: 0.8624 (m-30) cc_final: 0.8395 (m-30) REVERT: B 993 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7437 (t-90) REVERT: B 1099 ASP cc_start: 0.7683 (t0) cc_final: 0.7394 (t70) REVERT: B 1178 MET cc_start: 0.9591 (pmm) cc_final: 0.9244 (pmm) REVERT: B 1181 MET cc_start: 0.8465 (tmm) cc_final: 0.7912 (tmm) REVERT: B 1197 MET cc_start: 0.8847 (mpp) cc_final: 0.8399 (mpp) REVERT: B 1214 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.7036 (m110) REVERT: B 1299 MET cc_start: 0.8078 (ptp) cc_final: 0.7746 (ptp) REVERT: B 1323 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7295 (mm) REVERT: C 79 GLU cc_start: 0.8532 (mp0) cc_final: 0.7980 (mp0) outliers start: 64 outliers final: 37 residues processed: 222 average time/residue: 0.2155 time to fit residues: 68.2908 Evaluate side-chains 208 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 1059 ILE 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: 5.9990 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.107920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080576 restraints weight = 22332.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083972 restraints weight = 11992.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086344 restraints weight = 7904.609| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9506 Z= 0.284 Angle : 0.696 8.796 12947 Z= 0.354 Chirality : 0.050 0.209 1440 Planarity : 0.005 0.060 1683 Dihedral : 5.436 45.238 1292 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 6.72 % Allowed : 27.17 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.05 (0.26), residues: 382 loop : -1.59 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 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 0.001 ARG B1316 *********************** 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 245 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 177 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7961 (ptt90) REVERT: A 1956 ASN cc_start: 0.7228 (t0) cc_final: 0.6846 (m-40) REVERT: A 1974 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7939 (mmp80) REVERT: A 2036 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 638 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7100 (pp30) REVERT: B 685 MET cc_start: 0.5253 (mpp) cc_final: 0.4915 (mmp) REVERT: B 834 ASP cc_start: 0.8490 (t0) cc_final: 0.8149 (m-30) REVERT: B 883 LYS cc_start: 0.8773 (pttm) cc_final: 0.8483 (pttm) REVERT: B 993 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7416 (t-90) REVERT: B 998 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.6938 (ttp80) REVERT: B 1099 ASP cc_start: 0.7620 (t0) cc_final: 0.7139 (t0) REVERT: B 1178 MET cc_start: 0.9587 (pmm) cc_final: 0.9240 (pmm) REVERT: B 1181 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 1197 MET cc_start: 0.8840 (mpp) cc_final: 0.8192 (mpp) REVERT: B 1316 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8649 (ttp80) REVERT: B 1323 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7259 (mm) REVERT: C 79 GLU cc_start: 0.8501 (mp0) cc_final: 0.7943 (mp0) REVERT: C 119 MET cc_start: 0.8177 (mpp) cc_final: 0.7971 (mpp) outliers start: 68 outliers final: 41 residues processed: 222 average time/residue: 0.2028 time to fit residues: 63.9512 Evaluate side-chains 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 1953 LEU Chi-restraints excluded: chain A residue 2036 PHE 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 681 LEU 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 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 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 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 84 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1990 GLN A2007 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080046 restraints weight = 22229.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083378 restraints weight = 11964.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085745 restraints weight = 7910.397| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9506 Z= 0.311 Angle : 0.708 10.912 12947 Z= 0.360 Chirality : 0.050 0.232 1440 Planarity : 0.005 0.060 1683 Dihedral : 5.509 46.282 1292 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 6.92 % Allowed : 27.27 % Favored : 65.81 % 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: -2.12 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.02 (0.26), residues: 380 loop : -1.61 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 PHE 0.013 0.002 PHE B 483 TYR 0.019 0.002 TYR B1068 ARG 0.004 0.000 ARG B1316 *********************** 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 249 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1974 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7967 (mmp80) REVERT: A 1985 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7289 (ptp90) REVERT: A 2036 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7474 (t80) REVERT: B 834 ASP cc_start: 0.8499 (t0) cc_final: 0.8172 (m-30) REVERT: B 883 LYS cc_start: 0.8758 (pttm) cc_final: 0.8507 (pttm) REVERT: B 993 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7398 (t-90) REVERT: B 998 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.6969 (ttp80) REVERT: B 1056 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8193 (mmt-90) REVERT: B 1181 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: B 1197 MET cc_start: 0.8834 (mpp) cc_final: 0.8125 (mpp) REVERT: B 1323 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (mm) REVERT: C 79 GLU cc_start: 0.8526 (mp0) cc_final: 0.8051 (mp0) REVERT: C 119 MET cc_start: 0.8205 (mpp) cc_final: 0.7707 (mpp) outliers start: 70 outliers final: 49 residues processed: 230 average time/residue: 0.2141 time to fit residues: 69.2513 Evaluate side-chains 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL 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 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 776 VAL Chi-restraints excluded: chain B residue 778 LEU 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 993 HIS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 B 688 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.109264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081342 restraints weight = 22291.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084767 restraints weight = 12116.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087225 restraints weight = 8051.307| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9506 Z= 0.224 Angle : 0.687 8.191 12947 Z= 0.348 Chirality : 0.049 0.230 1440 Planarity : 0.005 0.068 1683 Dihedral : 5.350 46.501 1292 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.83 % Allowed : 29.05 % Favored : 65.12 % 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: -1.97 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -0.94 (0.26), residues: 386 loop : -1.53 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 PHE 0.014 0.001 PHE B 483 TYR 0.018 0.002 TYR B1068 ARG 0.015 0.000 ARG B1316 *********************** 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 250 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1952 GLN cc_start: 0.7666 (mt0) cc_final: 0.7187 (mp10) REVERT: A 1956 ASN cc_start: 0.7177 (t0) cc_final: 0.6856 (m-40) REVERT: A 2036 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 688 HIS cc_start: 0.6965 (t-90) cc_final: 0.6454 (t-170) REVERT: B 834 ASP cc_start: 0.8415 (t0) cc_final: 0.8148 (m-30) REVERT: B 846 ASP cc_start: 0.7889 (p0) cc_final: 0.7685 (m-30) REVERT: B 883 LYS cc_start: 0.8777 (pttm) cc_final: 0.8408 (pttm) REVERT: B 993 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7376 (t-90) REVERT: B 998 ARG cc_start: 0.7734 (mmt-90) cc_final: 0.6917 (ttp80) REVERT: B 1157 MET cc_start: 0.7876 (ppp) cc_final: 0.7664 (ppp) REVERT: B 1175 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6157 (t80) REVERT: B 1181 MET cc_start: 0.8282 (tmm) cc_final: 0.7646 (tmm) REVERT: B 1197 MET cc_start: 0.8798 (mpp) cc_final: 0.7995 (mpp) REVERT: B 1299 MET cc_start: 0.7887 (ptp) cc_final: 0.7643 (ptp) REVERT: B 1316 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8609 (ttp80) REVERT: B 1323 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7234 (mm) REVERT: C 79 GLU cc_start: 0.8450 (mp0) cc_final: 0.7968 (mp0) REVERT: C 119 MET cc_start: 0.8188 (mpp) cc_final: 0.7968 (mpp) outliers start: 59 outliers final: 41 residues processed: 232 average time/residue: 0.2112 time to fit residues: 69.1345 Evaluate side-chains 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 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 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 752 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1175 TYR 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 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 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: 7.9990 chunk 103 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** 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 = 0.3761 r_free = 0.3761 target = 0.108558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080670 restraints weight = 22715.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084118 restraints weight = 12249.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086560 restraints weight = 8114.998| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9506 Z= 0.254 Angle : 0.710 8.256 12947 Z= 0.358 Chirality : 0.050 0.205 1440 Planarity : 0.005 0.072 1683 Dihedral : 5.358 46.149 1292 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.03 % Allowed : 29.84 % Favored : 64.13 % 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: -1.97 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -0.96 (0.25), residues: 394 loop : -1.52 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.019 0.002 PHE B 683 TYR 0.031 0.002 TYR A2032 ARG 0.008 0.000 ARG B1316 *********************** 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 236 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1952 GLN cc_start: 0.7912 (mt0) cc_final: 0.7280 (mp10) REVERT: A 1956 ASN cc_start: 0.7059 (t0) cc_final: 0.6786 (m-40) REVERT: A 1965 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6980 (mtp-110) REVERT: A 1994 GLU cc_start: 0.8613 (tt0) cc_final: 0.8344 (tt0) REVERT: A 2036 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 683 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 685 MET cc_start: 0.4931 (mmp) cc_final: 0.4437 (mmp) REVERT: B 688 HIS cc_start: 0.7093 (t-90) cc_final: 0.6594 (t-170) REVERT: B 773 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7172 (mmm-85) REVERT: B 834 ASP cc_start: 0.8418 (t0) cc_final: 0.8169 (m-30) REVERT: B 883 LYS cc_start: 0.8748 (pttm) cc_final: 0.8342 (pttm) REVERT: B 993 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: B 998 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.6903 (ttp80) REVERT: B 1056 ARG cc_start: 0.8282 (mmm160) cc_final: 0.8012 (mmt-90) REVERT: B 1175 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6160 (t80) REVERT: B 1181 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7559 (tmm) REVERT: B 1197 MET cc_start: 0.8803 (mpp) cc_final: 0.7884 (mpp) REVERT: B 1216 LEU cc_start: 0.8249 (pt) cc_final: 0.7382 (tt) REVERT: B 1316 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8686 (ttp80) REVERT: B 1323 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7379 (mm) REVERT: C 79 GLU cc_start: 0.8482 (mp0) cc_final: 0.7988 (mp0) REVERT: C 119 MET cc_start: 0.8078 (mpp) cc_final: 0.7836 (mpp) outliers start: 61 outliers final: 46 residues processed: 219 average time/residue: 0.2109 time to fit residues: 65.1566 Evaluate side-chains 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE 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 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL 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 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 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 826 VAL Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 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: 0.8980 chunk 29 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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** ** 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 = 0.3748 r_free = 0.3748 target = 0.107779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079994 restraints weight = 23029.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083426 restraints weight = 12371.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085839 restraints weight = 8194.198| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9506 Z= 0.291 Angle : 0.735 11.379 12947 Z= 0.370 Chirality : 0.050 0.251 1440 Planarity : 0.005 0.069 1683 Dihedral : 5.471 46.574 1292 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.23 % Allowed : 29.74 % Favored : 64.03 % 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: -2.09 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.04 (0.25), residues: 401 loop : -1.57 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 PHE 0.016 0.002 PHE B 683 TYR 0.019 0.002 TYR B1068 ARG 0.007 0.000 ARG B1170 *********************** 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 232 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1952 GLN cc_start: 0.7949 (mt0) cc_final: 0.7551 (mt0) REVERT: A 1965 ARG cc_start: 0.7361 (ttp80) cc_final: 0.6987 (mtp-110) REVERT: A 1994 GLU cc_start: 0.8609 (tt0) cc_final: 0.8347 (tt0) REVERT: A 2036 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7388 (t80) REVERT: B 683 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8284 (t80) REVERT: B 688 HIS cc_start: 0.7155 (t-90) cc_final: 0.6629 (t-170) REVERT: B 834 ASP cc_start: 0.8474 (t0) cc_final: 0.8187 (m-30) REVERT: B 883 LYS cc_start: 0.8757 (pttm) cc_final: 0.8539 (pttm) REVERT: B 993 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7397 (t-90) REVERT: B 998 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.6861 (ttp80) REVERT: B 1056 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8081 (mmt-90) REVERT: B 1175 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6256 (t80) REVERT: B 1181 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7556 (tmm) REVERT: B 1197 MET cc_start: 0.8821 (mpp) cc_final: 0.7859 (mpp) REVERT: B 1216 LEU cc_start: 0.8284 (pt) cc_final: 0.7399 (tt) REVERT: B 1323 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7460 (mm) REVERT: C 79 GLU cc_start: 0.8494 (mp0) cc_final: 0.8001 (mp0) outliers start: 63 outliers final: 48 residues processed: 213 average time/residue: 0.1951 time to fit residues: 59.2323 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 2007 GLN 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 525 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 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 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 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.0000 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 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 A2007 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080877 restraints weight = 22728.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084315 restraints weight = 12289.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086753 restraints weight = 8151.859| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9506 Z= 0.263 Angle : 0.743 9.236 12947 Z= 0.371 Chirality : 0.051 0.236 1440 Planarity : 0.005 0.080 1683 Dihedral : 5.459 46.058 1292 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 6.23 % Allowed : 30.24 % Favored : 63.54 % 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: -2.06 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -0.99 (0.25), residues: 392 loop : -1.57 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.012 0.001 PHE B 483 TYR 0.019 0.002 TYR B1068 ARG 0.022 0.001 ARG B1316 *********************** 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 233 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1952 GLN cc_start: 0.7938 (mt0) cc_final: 0.7589 (mt0) REVERT: A 1956 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6548 (m-40) REVERT: A 1965 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6984 (mtp-110) REVERT: A 1994 GLU cc_start: 0.8597 (tt0) cc_final: 0.8330 (tt0) REVERT: A 2036 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 688 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6633 (t-170) REVERT: B 834 ASP cc_start: 0.8415 (t0) cc_final: 0.8188 (m-30) REVERT: B 883 LYS cc_start: 0.8771 (pttm) cc_final: 0.8542 (pttm) REVERT: B 993 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7320 (t-90) REVERT: B 998 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.6849 (ttp80) REVERT: B 1175 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6260 (t80) REVERT: B 1181 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7608 (tmm) REVERT: B 1197 MET cc_start: 0.8832 (mpp) cc_final: 0.8022 (mpp) REVERT: B 1216 LEU cc_start: 0.8292 (pt) cc_final: 0.7422 (tt) REVERT: B 1323 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7442 (mm) REVERT: C 79 GLU cc_start: 0.8481 (mp0) cc_final: 0.8010 (mp0) outliers start: 63 outliers final: 51 residues processed: 214 average time/residue: 0.2076 time to fit residues: 62.9991 Evaluate side-chains 223 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE 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 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL 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 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 688 HIS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 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 1287 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN ** B 638 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.109614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082036 restraints weight = 22523.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085509 restraints weight = 11994.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087945 restraints weight = 7884.697| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9506 Z= 0.226 Angle : 0.743 12.079 12947 Z= 0.369 Chirality : 0.050 0.227 1440 Planarity : 0.005 0.081 1683 Dihedral : 5.352 45.356 1292 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.53 % Allowed : 30.83 % Favored : 63.64 % 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: -2.05 (0.24), residues: 1181 helix: -4.67 (0.21), residues: 18 sheet: -0.90 (0.26), residues: 388 loop : -1.58 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.013 0.001 PHE B 483 TYR 0.019 0.002 TYR B1068 ARG 0.019 0.000 ARG B1316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1952 GLN cc_start: 0.7933 (mt0) cc_final: 0.7595 (mt0) REVERT: A 1956 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6500 (m-40) REVERT: A 1965 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6987 (mtp-110) REVERT: A 1994 GLU cc_start: 0.8580 (tt0) cc_final: 0.8318 (tt0) REVERT: A 2036 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7346 (t80) REVERT: A 2042 ASP cc_start: 0.8090 (m-30) cc_final: 0.7827 (m-30) REVERT: B 504 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7270 (pp20) REVERT: B 688 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6521 (t-170) REVERT: B 779 ASP cc_start: 0.7857 (m-30) cc_final: 0.7546 (t0) REVERT: B 883 LYS cc_start: 0.8790 (pttm) cc_final: 0.8538 (pttm) REVERT: B 993 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7081 (t-90) REVERT: B 998 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.6837 (ttp80) REVERT: B 1099 ASP cc_start: 0.7769 (t0) cc_final: 0.7518 (t0) REVERT: B 1175 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6205 (t80) REVERT: B 1181 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7609 (tmm) REVERT: B 1189 ASN cc_start: 0.8151 (p0) cc_final: 0.7869 (p0) REVERT: B 1197 MET cc_start: 0.8813 (mpp) cc_final: 0.8006 (mpp) REVERT: B 1216 LEU cc_start: 0.8286 (pt) cc_final: 0.7418 (tt) REVERT: B 1323 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7387 (mm) REVERT: C 79 GLU cc_start: 0.8486 (mp0) cc_final: 0.7989 (mp0) outliers start: 56 outliers final: 46 residues processed: 216 average time/residue: 0.2060 time to fit residues: 63.5341 Evaluate side-chains 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1942 VAL Chi-restraints excluded: chain A residue 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 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 688 HIS 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 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 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 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 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 1287 ILE Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.109444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081681 restraints weight = 22604.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085108 restraints weight = 12239.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087534 restraints weight = 8122.773| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9506 Z= 0.237 Angle : 0.750 12.376 12947 Z= 0.372 Chirality : 0.050 0.263 1440 Planarity : 0.005 0.071 1683 Dihedral : 5.328 45.156 1292 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.83 % Allowed : 30.73 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.67 (0.21), residues: 18 sheet: -0.86 (0.26), residues: 388 loop : -1.55 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.017 0.002 PHE C 71 TYR 0.019 0.002 TYR B1068 ARG 0.017 0.000 ARG B1316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.15 seconds wall clock time: 64 minutes 56.53 seconds (3896.53 seconds total)