Starting phenix.real_space_refine on Fri Nov 15 18:11:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_40241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_40241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_40241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_40241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/11_2024/8s9p_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.45, per 1000 atoms: 0.59 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: 2.43 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: 1.40 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: 4.17 Time building geometry restraints manager: 2.80 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: 0.550 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- 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 : 1.109 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: 0.2279 time to fit residues: 61.5884 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 : 1.138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 1.018 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: 0.8067 (mtm110) cc_final: 0.7780 (ptt90) REVERT: A 1983 GLU cc_start: 0.8291 (pp20) cc_final: 0.7989 (pp20) REVERT: A 2036 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 548 LEU cc_start: 0.8920 (tt) cc_final: 0.8627 (tt) REVERT: B 683 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 685 MET cc_start: 0.4800 (mpp) cc_final: 0.4535 (mmp) REVERT: B 687 ILE cc_start: 0.7169 (tp) cc_final: 0.6792 (pt) REVERT: B 688 HIS cc_start: 0.7276 (t-170) cc_final: 0.6720 (t-170) REVERT: B 834 ASP cc_start: 0.8130 (t0) cc_final: 0.7822 (t0) REVERT: B 998 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7264 (ttp80) REVERT: B 1099 ASP cc_start: 0.7530 (t0) cc_final: 0.7234 (t70) REVERT: B 1153 LEU cc_start: 0.8598 (mt) cc_final: 0.8194 (pp) REVERT: B 1181 MET cc_start: 0.8535 (tmm) cc_final: 0.8204 (tmm) REVERT: B 1197 MET cc_start: 0.8750 (mpp) cc_final: 0.8490 (mpp) REVERT: B 1216 LEU cc_start: 0.8286 (pt) cc_final: 0.7638 (tt) REVERT: C 36 THR cc_start: 0.8875 (m) cc_final: 0.8661 (p) REVERT: C 79 GLU cc_start: 0.8388 (mp0) cc_final: 0.8021 (mp0) REVERT: C 118 LYS cc_start: 0.8268 (mptt) cc_final: 0.7658 (pttt) outliers start: 42 outliers final: 17 residues processed: 223 average time/residue: 0.2266 time to fit residues: 70.3411 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 : 1.049 ------------------------------------------------------------------------------- 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 59 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 0.0570 chunk 85 optimal weight: 10.0000 overall best weight: 2.2100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9506 Z= 0.275 Angle : 0.685 8.829 12947 Z= 0.351 Chirality : 0.049 0.202 1440 Planarity : 0.005 0.059 1683 Dihedral : 5.305 42.682 1292 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.83 % Allowed : 26.98 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.01 (0.26), residues: 374 loop : -1.54 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B1186 HIS 0.004 0.001 HIS A2048 PHE 0.015 0.002 PHE B 746 TYR 0.019 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 243 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1876 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7851 (ptt90) REVERT: A 2036 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7254 (t80) REVERT: B 683 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8044 (t80) REVERT: B 685 MET cc_start: 0.4824 (mpp) cc_final: 0.4586 (mmp) REVERT: B 687 ILE cc_start: 0.7300 (tp) cc_final: 0.6909 (pt) REVERT: B 834 ASP cc_start: 0.8360 (t0) cc_final: 0.8136 (m-30) REVERT: B 993 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: B 998 ARG cc_start: 0.7793 (mmt-90) cc_final: 0.6983 (ttp80) REVERT: B 1099 ASP cc_start: 0.7608 (t0) cc_final: 0.7123 (t0) REVERT: B 1178 MET cc_start: 0.9587 (pmm) cc_final: 0.9243 (pmm) REVERT: B 1181 MET cc_start: 0.8438 (tmm) cc_final: 0.7893 (tmm) REVERT: B 1197 MET cc_start: 0.8778 (mpp) cc_final: 0.8269 (mpp) REVERT: B 1214 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6915 (m110) REVERT: B 1299 MET cc_start: 0.7963 (ptp) cc_final: 0.7701 (ptp) REVERT: B 1323 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7240 (mm) REVERT: C 79 GLU cc_start: 0.8546 (mp0) cc_final: 0.7995 (mp0) outliers start: 59 outliers final: 34 residues processed: 220 average time/residue: 0.2119 time to fit residues: 66.1423 Evaluate side-chains 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 603 LEU Chi-restraints excluded: chain B residue 683 PHE 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 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 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 51 VAL 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 105 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2161 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= 0.254 Angle : 0.687 8.989 12947 Z= 0.346 Chirality : 0.049 0.200 1440 Planarity : 0.005 0.058 1683 Dihedral : 5.286 44.237 1292 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.93 % Allowed : 28.56 % Favored : 65.51 % 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: -4.53 (0.22), residues: 12 sheet: -0.95 (0.26), residues: 380 loop : -1.53 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B1186 HIS 0.004 0.001 HIS B 562 PHE 0.014 0.002 PHE B 483 TYR 0.018 0.001 TYR B1068 ARG 0.012 0.000 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 239 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.064 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: 0.8239 (mtm110) cc_final: 0.7869 (ptt90) REVERT: A 1956 ASN cc_start: 0.7125 (t0) cc_final: 0.6901 (m-40) REVERT: A 1974 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7931 (mmp80) REVERT: A 2036 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 638 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.7071 (pp30) REVERT: B 683 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 685 MET cc_start: 0.5030 (mpp) cc_final: 0.4774 (mmp) REVERT: B 834 ASP cc_start: 0.8389 (t0) cc_final: 0.8126 (m-30) REVERT: B 993 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7335 (t-90) REVERT: B 998 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.6936 (ttp80) REVERT: B 1080 MET cc_start: 0.5831 (mpp) cc_final: 0.5432 (mpp) REVERT: B 1099 ASP cc_start: 0.7633 (t0) cc_final: 0.7081 (t0) REVERT: B 1178 MET cc_start: 0.9580 (pmm) cc_final: 0.9247 (pmm) REVERT: B 1181 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: B 1197 MET cc_start: 0.8837 (mpp) cc_final: 0.8211 (mpp) REVERT: B 1214 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6892 (m110) REVERT: B 1316 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8638 (ttp80) REVERT: B 1323 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 63 ARG cc_start: 0.8775 (ttt180) cc_final: 0.8396 (ttt180) REVERT: C 79 GLU cc_start: 0.8529 (mp0) cc_final: 0.7972 (mp0) REVERT: C 119 MET cc_start: 0.8190 (mpp) cc_final: 0.7897 (mpp) outliers start: 60 outliers final: 37 residues processed: 218 average time/residue: 0.1922 time to fit residues: 60.2911 Evaluate side-chains 218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 2036 PHE 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 591 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 732 SER 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 845 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 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 1105 ILE Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1214 ASN Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 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 51 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** B1271 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9506 Z= 0.295 Angle : 0.696 11.015 12947 Z= 0.353 Chirality : 0.049 0.191 1440 Planarity : 0.005 0.059 1683 Dihedral : 5.378 45.734 1292 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.21 % Allowed : 27.08 % Favored : 65.71 % 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: -2.08 (0.24), residues: 1181 helix: -4.53 (0.22), residues: 12 sheet: -1.04 (0.25), residues: 388 loop : -1.56 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B1186 HIS 0.004 0.001 HIS B 562 PHE 0.014 0.002 PHE B 483 TYR 0.018 0.002 TYR B 654 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 251 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1956 ASN cc_start: 0.7123 (t0) cc_final: 0.6894 (m-40) REVERT: A 1974 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7976 (mmp80) REVERT: A 1985 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7264 (ptp90) REVERT: A 2036 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7232 (t80) REVERT: B 685 MET cc_start: 0.5191 (mpp) cc_final: 0.4926 (mmp) REVERT: B 687 ILE cc_start: 0.7416 (tp) cc_final: 0.6906 (pt) REVERT: B 834 ASP cc_start: 0.8446 (t0) cc_final: 0.8147 (m-30) REVERT: B 993 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: B 998 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.6948 (ttp80) REVERT: B 1099 ASP cc_start: 0.7648 (t0) cc_final: 0.7139 (t0) REVERT: B 1175 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6197 (t80) REVERT: B 1178 MET cc_start: 0.9593 (pmm) cc_final: 0.9051 (pmm) REVERT: B 1181 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7684 (tmm) REVERT: B 1197 MET cc_start: 0.8840 (mpp) cc_final: 0.8076 (mpp) REVERT: C 63 ARG cc_start: 0.8777 (ttt180) cc_final: 0.8367 (ttt180) REVERT: C 79 GLU cc_start: 0.8560 (mp0) cc_final: 0.8101 (mp0) REVERT: C 119 MET cc_start: 0.8199 (mpp) cc_final: 0.7675 (mpp) outliers start: 73 outliers final: 46 residues processed: 228 average time/residue: 0.2111 time to fit residues: 68.1810 Evaluate side-chains 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 1953 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 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 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 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 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 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 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 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 101 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.0030 chunk 27 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- 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 B 688 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9506 Z= 0.236 Angle : 0.687 8.227 12947 Z= 0.346 Chirality : 0.049 0.233 1440 Planarity : 0.005 0.058 1683 Dihedral : 5.304 47.101 1292 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.03 % Allowed : 28.56 % Favored : 65.42 % 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: -1.92 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -0.92 (0.26), residues: 371 loop : -1.48 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B1186 HIS 0.003 0.001 HIS A2048 PHE 0.014 0.002 PHE C 71 TYR 0.017 0.002 TYR B 654 ARG 0.016 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 247 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1985 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7360 (ptp-170) REVERT: A 2036 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7234 (t80) REVERT: B 688 HIS cc_start: 0.7019 (t-90) cc_final: 0.6505 (t-170) REVERT: B 834 ASP cc_start: 0.8365 (t0) cc_final: 0.8117 (m-30) REVERT: B 993 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: B 998 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.6932 (ttp80) REVERT: B 1175 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 1178 MET cc_start: 0.9587 (pmm) cc_final: 0.9225 (pmm) REVERT: B 1181 MET cc_start: 0.8340 (tmm) cc_final: 0.7677 (tmm) REVERT: B 1197 MET cc_start: 0.8793 (mpp) cc_final: 0.7962 (mpp) REVERT: B 1205 LEU cc_start: 0.8599 (mm) cc_final: 0.8205 (mm) REVERT: B 1216 LEU cc_start: 0.8269 (pt) cc_final: 0.7462 (tt) REVERT: B 1316 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8622 (ttp80) REVERT: C 63 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8352 (ttt180) REVERT: C 79 GLU cc_start: 0.8491 (mp0) cc_final: 0.8027 (mp0) REVERT: C 119 MET cc_start: 0.8298 (mpp) cc_final: 0.8069 (mpp) outliers start: 61 outliers final: 44 residues processed: 230 average time/residue: 0.2202 time to fit residues: 70.6810 Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 THR 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 C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1990 GLN B 601 ASN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9506 Z= 0.180 Angle : 0.708 13.438 12947 Z= 0.351 Chirality : 0.049 0.243 1440 Planarity : 0.005 0.059 1683 Dihedral : 5.148 46.284 1292 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.25 % Allowed : 31.42 % Favored : 64.33 % 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: -1.91 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -0.99 (0.26), residues: 369 loop : -1.44 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B1186 HIS 0.003 0.000 HIS A2048 PHE 0.010 0.001 PHE B 683 TYR 0.017 0.002 TYR B 654 ARG 0.007 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 231 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.011 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 2032 TYR cc_start: 0.8286 (m-80) cc_final: 0.7837 (m-80) REVERT: A 2036 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7125 (t80) REVERT: B 493 LEU cc_start: 0.8518 (tp) cc_final: 0.8066 (tp) REVERT: B 688 HIS cc_start: 0.6943 (t-90) cc_final: 0.6462 (t-170) REVERT: B 993 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7266 (t-90) REVERT: B 998 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.6882 (ttp80) REVERT: B 1175 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6114 (t80) REVERT: B 1178 MET cc_start: 0.9563 (OUTLIER) cc_final: 0.9339 (pmm) REVERT: B 1181 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: B 1197 MET cc_start: 0.8736 (mpp) cc_final: 0.7902 (mpp) REVERT: B 1205 LEU cc_start: 0.8656 (mm) cc_final: 0.8286 (mm) REVERT: B 1216 LEU cc_start: 0.8192 (pt) cc_final: 0.7376 (tt) REVERT: C 63 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8340 (ttt180) REVERT: C 79 GLU cc_start: 0.8463 (mp0) cc_final: 0.7983 (mp0) REVERT: C 119 MET cc_start: 0.8128 (mpp) cc_final: 0.7868 (mpp) outliers start: 43 outliers final: 28 residues processed: 213 average time/residue: 0.2225 time to fit residues: 66.5486 Evaluate side-chains 207 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 1928 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 683 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 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 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 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 1296 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR 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 67 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 0.0040 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9506 Z= 0.193 Angle : 0.713 14.631 12947 Z= 0.354 Chirality : 0.049 0.231 1440 Planarity : 0.005 0.059 1683 Dihedral : 5.116 46.210 1292 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.74 % Allowed : 31.52 % Favored : 63.74 % 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: -1.86 (0.24), residues: 1181 helix: -4.69 (0.36), residues: 6 sheet: -0.84 (0.27), residues: 358 loop : -1.45 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.018 0.001 PHE B 683 TYR 0.032 0.002 TYR A1941 ARG 0.015 0.000 ARG B1316 *********************** 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 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1965 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6997 (mtp-110) REVERT: A 2036 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7151 (t80) REVERT: B 493 LEU cc_start: 0.8551 (tp) cc_final: 0.8074 (tp) REVERT: B 564 MET cc_start: 0.8550 (mmm) cc_final: 0.8317 (mmm) REVERT: B 598 PHE cc_start: 0.8734 (t80) cc_final: 0.8300 (t80) REVERT: B 683 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 685 MET cc_start: 0.4658 (mmp) cc_final: 0.4062 (mmt) REVERT: B 688 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6491 (t-170) REVERT: B 779 ASP cc_start: 0.7696 (m-30) cc_final: 0.7338 (t0) REVERT: B 883 LYS cc_start: 0.8705 (pttm) cc_final: 0.7760 (pttp) REVERT: B 993 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7121 (t-90) REVERT: B 998 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.6870 (ttp80) REVERT: B 1008 MET cc_start: 0.9062 (ptp) cc_final: 0.8831 (ptp) REVERT: B 1175 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6082 (t80) REVERT: B 1178 MET cc_start: 0.9563 (pmm) cc_final: 0.9309 (pmm) REVERT: B 1181 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: B 1197 MET cc_start: 0.8767 (mpp) cc_final: 0.7826 (mpp) REVERT: B 1205 LEU cc_start: 0.8649 (mm) cc_final: 0.8302 (mm) REVERT: B 1216 LEU cc_start: 0.8202 (pt) cc_final: 0.7417 (tt) REVERT: C 37 VAL cc_start: 0.8864 (m) cc_final: 0.8518 (p) REVERT: C 63 ARG cc_start: 0.8757 (ttt180) cc_final: 0.8315 (ttt180) REVERT: C 79 GLU cc_start: 0.8479 (mp0) cc_final: 0.8177 (mp0) REVERT: C 119 MET cc_start: 0.7929 (mpp) cc_final: 0.7674 (mpp) outliers start: 48 outliers final: 35 residues processed: 209 average time/residue: 0.2168 time to fit residues: 63.9039 Evaluate side-chains 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 1928 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 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 688 HIS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1175 TYR Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1296 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 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 98 optimal weight: 0.0040 chunk 105 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9506 Z= 0.227 Angle : 0.719 12.807 12947 Z= 0.359 Chirality : 0.049 0.270 1440 Planarity : 0.005 0.073 1683 Dihedral : 5.174 46.526 1292 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.14 % Allowed : 31.03 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.24), residues: 1181 helix: -4.69 (0.35), residues: 6 sheet: -0.81 (0.27), residues: 359 loop : -1.41 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B1186 HIS 0.003 0.001 HIS A1981 PHE 0.019 0.001 PHE B 683 TYR 0.028 0.002 TYR A1941 ARG 0.017 0.000 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 229 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1974 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7985 (mmp80) REVERT: A 1983 GLU cc_start: 0.8526 (pp20) cc_final: 0.8252 (tm-30) REVERT: A 1984 GLN cc_start: 0.8882 (mt0) cc_final: 0.8238 (mt0) REVERT: A 2036 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7135 (t80) REVERT: B 493 LEU cc_start: 0.8596 (tp) cc_final: 0.8085 (tp) REVERT: B 598 PHE cc_start: 0.8722 (t80) cc_final: 0.8265 (t80) REVERT: B 683 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 688 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6590 (t-170) REVERT: B 779 ASP cc_start: 0.7720 (m-30) cc_final: 0.7402 (t0) REVERT: B 993 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7174 (t-90) REVERT: B 998 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7058 (ttp80) REVERT: B 1008 MET cc_start: 0.9078 (ptp) cc_final: 0.8843 (ptp) REVERT: B 1175 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6170 (t80) REVERT: B 1178 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.9334 (pmm) REVERT: B 1181 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7587 (tmm) REVERT: B 1197 MET cc_start: 0.8784 (mpp) cc_final: 0.7852 (mpp) REVERT: B 1205 LEU cc_start: 0.8668 (mm) cc_final: 0.8328 (mm) REVERT: B 1216 LEU cc_start: 0.8239 (pt) cc_final: 0.7432 (tt) REVERT: C 63 ARG cc_start: 0.8765 (ttt180) cc_final: 0.8286 (ttt180) REVERT: C 79 GLU cc_start: 0.8511 (mp0) cc_final: 0.8205 (mp0) outliers start: 52 outliers final: 39 residues processed: 211 average time/residue: 0.2224 time to fit residues: 66.0918 Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 1928 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 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 688 HIS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 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 1296 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 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 111 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9506 Z= 0.208 Angle : 0.739 17.288 12947 Z= 0.364 Chirality : 0.049 0.261 1440 Planarity : 0.005 0.085 1683 Dihedral : 5.134 45.981 1292 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.55 % Allowed : 31.62 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.24), residues: 1181 helix: -4.68 (0.36), residues: 6 sheet: -0.83 (0.27), residues: 360 loop : -1.38 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B1186 HIS 0.003 0.001 HIS B 688 PHE 0.016 0.001 PHE C 71 TYR 0.023 0.002 TYR A1941 ARG 0.021 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 225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.109 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 1984 GLN cc_start: 0.8899 (mt0) cc_final: 0.8566 (mt0) REVERT: A 2036 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7187 (t80) REVERT: B 493 LEU cc_start: 0.8569 (tp) cc_final: 0.8070 (tp) REVERT: B 598 PHE cc_start: 0.8720 (t80) cc_final: 0.8290 (t80) REVERT: B 683 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 688 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6527 (t-170) REVERT: B 779 ASP cc_start: 0.7688 (m-30) cc_final: 0.7361 (t0) REVERT: B 993 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: B 998 ARG cc_start: 0.7710 (mmt-90) cc_final: 0.6901 (ttp80) REVERT: B 1008 MET cc_start: 0.9078 (ptp) cc_final: 0.8842 (ptp) REVERT: B 1099 ASP cc_start: 0.7793 (t0) cc_final: 0.7545 (t0) REVERT: B 1175 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.6186 (t80) REVERT: B 1181 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: B 1197 MET cc_start: 0.8784 (mpp) cc_final: 0.7879 (mpp) REVERT: B 1205 LEU cc_start: 0.8671 (mm) cc_final: 0.8359 (mm) REVERT: B 1216 LEU cc_start: 0.8227 (pt) cc_final: 0.7428 (tt) REVERT: C 63 ARG cc_start: 0.8778 (ttt180) cc_final: 0.8328 (ttt180) REVERT: C 79 GLU cc_start: 0.8506 (mp0) cc_final: 0.8184 (mp0) outliers start: 46 outliers final: 39 residues processed: 208 average time/residue: 0.2153 time to fit residues: 63.1079 Evaluate side-chains 217 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 1928 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 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 688 HIS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1030 CYS Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 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 1296 LEU Chi-restraints excluded: chain B residue 1335 CYS 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 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 98 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.109041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081896 restraints weight = 22235.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085252 restraints weight = 11969.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087602 restraints weight = 7875.858| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9506 Z= 0.274 Angle : 0.771 17.338 12947 Z= 0.381 Chirality : 0.050 0.270 1440 Planarity : 0.005 0.092 1683 Dihedral : 5.305 46.244 1292 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.94 % Allowed : 31.23 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.25), residues: 1181 helix: -4.80 (0.29), residues: 12 sheet: -0.96 (0.27), residues: 372 loop : -1.43 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP B1186 HIS 0.002 0.001 HIS B 562 PHE 0.013 0.002 PHE B 746 TYR 0.025 0.002 TYR A1941 ARG 0.021 0.001 ARG B1316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.38 seconds wall clock time: 41 minutes 55.12 seconds (2515.12 seconds total)