Starting phenix.real_space_refine on Thu Mar 14 17:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/03_2024/8s9p_40241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/03_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_40241/03_2024/8s9p_40241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/03_2024/8s9p_40241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/03_2024/8s9p_40241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s9p_40241/03_2024/8s9p_40241.pdb" } 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 Residue "A TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1887": "OE1" <-> "OE2" Residue "A ASP 2009": "OD1" <-> "OD2" Residue "A TYR 2032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B ASP 628": "OD1" <-> "OD2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 771": "OD1" <-> "OD2" Residue "B ASP 791": "OD1" <-> "OD2" Residue "B ASP 834": "OD1" <-> "OD2" Residue "B ASP 859": "OD1" <-> "OD2" Residue "B TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 928": "OE1" <-> "OE2" Residue "B PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 956": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ASP 1132": "OD1" <-> "OD2" Residue "B TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1298": "OD1" <-> "OD2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.35, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.76 Conformation dependent library (CDL) restraints added in 2.0 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: 1.25 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: 4.14 Time building geometry restraints manager: 4.09 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: 97.09 - 104.49: 169 104.49 - 111.88: 4610 111.88 - 119.27: 3266 119.27 - 126.66: 4689 126.66 - 134.05: 213 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 2.520 nonbonded pdb=" OD2 ASP B 911 " pdb=" OG SER B 914 " model vdw 2.108 2.440 nonbonded pdb=" NH1 ARG B 749 " pdb=" OG SER B 774 " model vdw 2.140 2.520 nonbonded pdb=" OH TYR B 613 " pdb=" NZ LYS B 668 " model vdw 2.187 2.520 nonbonded pdb=" N GLU B 623 " pdb=" OE1 GLU B 623 " model vdw 2.208 2.520 ... (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 ========== 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: 0.570 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: 3.340 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.880 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.203 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: 0.2229 time to fit residues: 60.0383 Evaluate side-chains 190 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 6.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 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: 0.7748 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9506 Z= 0.290 Angle : 0.685 8.875 12947 Z= 0.359 Chirality : 0.050 0.188 1440 Planarity : 0.005 0.063 1683 Dihedral : 6.045 47.290 1312 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.30 % Favored : 91.62 % Rotamer: Outliers : 5.34 % Allowed : 29.15 % 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: -2.03 (0.24), residues: 1181 helix: -3.38 (1.19), residues: 12 sheet: -1.10 (0.25), residues: 411 loop : -1.48 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1186 HIS 0.005 0.001 HIS B 642 PHE 0.019 0.002 PHE B 949 TYR 0.021 0.002 TYR B1068 ARG 0.004 0.000 ARG A1977 *********************** 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 238 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2036 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 449 ASP cc_start: 0.7584 (m-30) cc_final: 0.7217 (m-30) REVERT: B 683 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 685 MET cc_start: 0.4781 (mpp) cc_final: 0.4474 (mmt) REVERT: B 688 HIS cc_start: 0.7399 (t-170) cc_final: 0.6923 (t-170) REVERT: B 1099 ASP cc_start: 0.7607 (t0) cc_final: 0.7264 (t70) REVERT: B 1181 MET cc_start: 0.8630 (tmm) cc_final: 0.8283 (tmm) REVERT: B 1197 MET cc_start: 0.8618 (mpp) cc_final: 0.8357 (mpp) REVERT: C 79 GLU cc_start: 0.8447 (mp0) cc_final: 0.8059 (mp0) REVERT: C 118 LYS cc_start: 0.8347 (mptt) cc_final: 0.7800 (pttt) outliers start: 54 outliers final: 32 residues processed: 218 average time/residue: 0.2066 time to fit residues: 62.8089 Evaluate side-chains 205 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1925 THR 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 559 ILE Chi-restraints excluded: chain B residue 683 PHE 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 852 VAL Chi-restraints excluded: chain B residue 906 ASN Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1129 LEU Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 85 optimal weight: 8.9990 overall best weight: 1.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN B 638 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 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: 0.7742 moved from start: 0.1587 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= 0.239 Angle : 0.660 9.011 12947 Z= 0.339 Chirality : 0.049 0.198 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.299 45.722 1293 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.21 % Favored : 91.70 % Rotamer: Outliers : 7.41 % Allowed : 27.67 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.65 (0.22), residues: 18 sheet: -1.05 (0.25), residues: 406 loop : -1.59 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B1186 HIS 0.005 0.001 HIS B 562 PHE 0.016 0.002 PHE B 483 TYR 0.018 0.001 TYR B1068 ARG 0.003 0.000 ARG A2047 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 178 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2036 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 449 ASP cc_start: 0.7672 (m-30) cc_final: 0.7251 (m-30) REVERT: B 638 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7090 (pp30) REVERT: B 683 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 687 ILE cc_start: 0.7190 (tp) cc_final: 0.6713 (pt) REVERT: B 688 HIS cc_start: 0.7419 (t-170) cc_final: 0.6992 (t-170) REVERT: B 993 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7405 (t-90) REVERT: B 998 ARG cc_start: 0.7804 (mmt-90) cc_final: 0.6993 (ttp80) REVERT: B 1099 ASP cc_start: 0.7647 (t0) cc_final: 0.7334 (t70) REVERT: B 1181 MET cc_start: 0.8519 (tmm) cc_final: 0.7964 (tmm) REVERT: B 1197 MET cc_start: 0.8667 (mpp) cc_final: 0.8247 (mpp) REVERT: B 1214 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6969 (m110) REVERT: B 1273 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7764 (mtm-85) REVERT: B 1323 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7243 (mm) REVERT: C 79 GLU cc_start: 0.8445 (mp0) cc_final: 0.8062 (mp0) outliers start: 75 outliers final: 43 residues processed: 234 average time/residue: 0.2030 time to fit residues: 66.4364 Evaluate side-chains 218 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1998 THR 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 516 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 833 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 906 ASN 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 1047 MET Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1129 LEU Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1214 ASN Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1273 ARG 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 36 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1984 GLN A1990 GLN ** A1993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9506 Z= 0.484 Angle : 0.778 8.765 12947 Z= 0.404 Chirality : 0.052 0.241 1440 Planarity : 0.006 0.064 1683 Dihedral : 5.880 48.637 1292 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.50 % Favored : 89.42 % Rotamer: Outliers : 9.49 % Allowed : 26.68 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1181 helix: -4.64 (0.22), residues: 18 sheet: -1.41 (0.25), residues: 386 loop : -1.76 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B1186 HIS 0.007 0.001 HIS B 562 PHE 0.015 0.002 PHE B 746 TYR 0.023 0.002 TYR B1068 ARG 0.005 0.001 ARG B1170 *********************** 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 268 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 172 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1994 GLU cc_start: 0.8398 (tt0) cc_final: 0.8145 (tt0) REVERT: A 2036 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 638 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7313 (pp30) REVERT: B 687 ILE cc_start: 0.7281 (tp) cc_final: 0.6776 (pt) REVERT: B 773 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7400 (mmm-85) REVERT: B 791 ASP cc_start: 0.8529 (m-30) cc_final: 0.8310 (m-30) REVERT: B 993 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7501 (t-90) REVERT: B 1099 ASP cc_start: 0.7751 (t0) cc_final: 0.7437 (t70) REVERT: B 1127 ASP cc_start: 0.7457 (t0) cc_final: 0.7190 (t0) REVERT: B 1181 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7950 (tmm) REVERT: B 1197 MET cc_start: 0.8826 (mpp) cc_final: 0.8369 (mpp) REVERT: B 1227 TRP cc_start: 0.7871 (p90) cc_final: 0.6861 (p90) REVERT: B 1299 MET cc_start: 0.8379 (ptp) cc_final: 0.7836 (ptp) REVERT: B 1323 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7452 (mm) REVERT: C 79 GLU cc_start: 0.8551 (mp0) cc_final: 0.8153 (mp0) REVERT: C 110 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6759 (tp30) REVERT: C 118 LYS cc_start: 0.8041 (mptt) cc_final: 0.7775 (tmtt) outliers start: 96 outliers final: 55 residues processed: 240 average time/residue: 0.2042 time to fit residues: 69.7986 Evaluate side-chains 222 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 1998 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 561 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 664 ASN 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 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 833 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 906 ASN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 993 HIS Chi-restraints excluded: chain B residue 1047 MET Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 36 THR 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 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 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: 0.7725 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9506 Z= 0.197 Angle : 0.689 11.109 12947 Z= 0.346 Chirality : 0.050 0.218 1440 Planarity : 0.005 0.062 1683 Dihedral : 5.369 47.059 1292 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 5.43 % Allowed : 31.42 % Favored : 63.14 % 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: -2.21 (0.24), residues: 1181 helix: -4.66 (0.21), residues: 18 sheet: -1.13 (0.25), residues: 397 loop : -1.62 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B1186 HIS 0.003 0.001 HIS A2048 PHE 0.014 0.001 PHE B 483 TYR 0.016 0.001 TYR B1068 ARG 0.003 0.000 ARG B 749 *********************** 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 232 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 177 time to evaluate : 1.161 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: 0.7088 (t0) cc_final: 0.6860 (m-40) REVERT: A 2036 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 638 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: B 687 ILE cc_start: 0.7245 (tp) cc_final: 0.6800 (pt) REVERT: B 993 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7486 (t-90) REVERT: B 998 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.6952 (ttp80) REVERT: B 1153 LEU cc_start: 0.8652 (mt) cc_final: 0.7842 (pp) REVERT: B 1181 MET cc_start: 0.8363 (tmm) cc_final: 0.7738 (tmm) REVERT: B 1197 MET cc_start: 0.8803 (mpp) cc_final: 0.8204 (mpp) REVERT: B 1323 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7505 (mm) REVERT: C 43 GLU cc_start: 0.7653 (pm20) cc_final: 0.7388 (pm20) REVERT: C 79 GLU cc_start: 0.8408 (mp0) cc_final: 0.8008 (mp0) outliers start: 55 outliers final: 34 residues processed: 220 average time/residue: 0.1947 time to fit residues: 61.0946 Evaluate side-chains 201 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 591 ILE 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 837 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 906 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 965 THR 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 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS 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 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9506 Z= 0.336 Angle : 0.707 8.496 12947 Z= 0.360 Chirality : 0.050 0.203 1440 Planarity : 0.005 0.063 1683 Dihedral : 5.532 48.273 1292 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.16 % Favored : 89.75 % Rotamer: Outliers : 7.31 % Allowed : 29.45 % Favored : 63.24 % 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: -2.34 (0.24), residues: 1181 helix: -4.67 (0.21), residues: 18 sheet: -1.26 (0.25), residues: 400 loop : -1.69 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1186 HIS 0.003 0.001 HIS B 562 PHE 0.012 0.002 PHE B 483 TYR 0.019 0.002 TYR B1068 ARG 0.004 0.000 ARG A1977 *********************** 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 244 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1994 GLU cc_start: 0.8373 (tt0) cc_final: 0.7894 (tt0) REVERT: A 2036 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 493 LEU cc_start: 0.8705 (tp) cc_final: 0.8323 (tp) REVERT: B 584 MET cc_start: 0.8562 (ptp) cc_final: 0.8132 (ptp) REVERT: B 687 ILE cc_start: 0.7247 (tp) cc_final: 0.6729 (pt) REVERT: B 773 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7368 (mmm-85) REVERT: B 990 MET cc_start: 0.8710 (tpp) cc_final: 0.8497 (tpp) REVERT: B 993 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7459 (t-90) REVERT: B 998 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7022 (ttp80) REVERT: B 1127 ASP cc_start: 0.7439 (t0) cc_final: 0.7138 (t0) REVERT: B 1181 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7727 (tmm) REVERT: B 1197 MET cc_start: 0.8808 (mpp) cc_final: 0.8162 (mpp) REVERT: B 1323 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7586 (mm) REVERT: C 79 GLU cc_start: 0.8509 (mp0) cc_final: 0.8230 (mp0) outliers start: 74 outliers final: 54 residues processed: 221 average time/residue: 0.2036 time to fit residues: 65.0905 Evaluate side-chains 221 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 162 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1896 VAL Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1983 GLU Chi-restraints excluded: chain A residue 1993 ASN Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 559 ILE 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 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 773 ARG Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 906 ASN 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 1047 MET Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1195 SER Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1279 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1993 ASN B 638 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 HIS B1109 ASN B1114 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9506 Z= 0.178 Angle : 0.680 8.240 12947 Z= 0.339 Chirality : 0.049 0.225 1440 Planarity : 0.004 0.062 1683 Dihedral : 5.214 46.028 1292 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.84 % Allowed : 32.71 % Favored : 62.45 % 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: -4.67 (0.21), residues: 18 sheet: -0.92 (0.26), residues: 387 loop : -1.58 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1186 HIS 0.004 0.001 HIS A2048 PHE 0.013 0.001 PHE B 483 TYR 0.018 0.001 TYR B1068 ARG 0.002 0.000 ARG A2047 *********************** 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 229 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1893 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 1956 ASN cc_start: 0.7130 (t0) cc_final: 0.6817 (m-40) REVERT: A 2036 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 584 MET cc_start: 0.8326 (ptp) cc_final: 0.8011 (ptp) REVERT: B 993 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: B 998 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.6961 (ttp80) REVERT: B 1099 ASP cc_start: 0.7705 (t0) cc_final: 0.7451 (t0) REVERT: B 1127 ASP cc_start: 0.7511 (t0) cc_final: 0.7232 (t0) REVERT: B 1153 LEU cc_start: 0.8421 (mt) cc_final: 0.8137 (mt) REVERT: B 1157 MET cc_start: 0.7657 (ppp) cc_final: 0.7450 (ppp) REVERT: B 1181 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7615 (tmm) REVERT: B 1197 MET cc_start: 0.8765 (mpp) cc_final: 0.8049 (mpp) REVERT: B 1216 LEU cc_start: 0.8179 (pt) cc_final: 0.7261 (tt) REVERT: B 1323 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7343 (mm) REVERT: C 79 GLU cc_start: 0.8411 (mp0) cc_final: 0.8124 (mp0) outliers start: 49 outliers final: 34 residues processed: 216 average time/residue: 0.1987 time to fit residues: 61.6383 Evaluate side-chains 204 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG 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 1953 LEU Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 837 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 965 THR Chi-restraints excluded: chain B residue 993 HIS 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 1176 HIS Chi-restraints excluded: chain B residue 1181 MET 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 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 102 optimal weight: 0.1980 chunk 108 optimal weight: 0.5980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 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: 0.7725 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9506 Z= 0.216 Angle : 0.687 8.613 12947 Z= 0.343 Chirality : 0.049 0.221 1440 Planarity : 0.004 0.061 1683 Dihedral : 5.218 46.758 1292 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.43 % Allowed : 32.31 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.66 (0.21), residues: 18 sheet: -1.01 (0.26), residues: 390 loop : -1.55 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP B1186 HIS 0.003 0.001 HIS A1981 PHE 0.014 0.001 PHE B 483 TYR 0.017 0.001 TYR B1068 ARG 0.005 0.000 ARG A1982 *********************** 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 233 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1956 ASN cc_start: 0.7067 (t0) cc_final: 0.6729 (m-40) REVERT: A 2036 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 584 MET cc_start: 0.8329 (ptp) cc_final: 0.7892 (ptp) REVERT: B 779 ASP cc_start: 0.7714 (m-30) cc_final: 0.7446 (t0) REVERT: B 993 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: B 998 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.7104 (ttp80) REVERT: B 1099 ASP cc_start: 0.7722 (t0) cc_final: 0.7420 (t0) REVERT: B 1127 ASP cc_start: 0.7536 (t0) cc_final: 0.7246 (t0) REVERT: B 1181 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: B 1197 MET cc_start: 0.8759 (mpp) cc_final: 0.8031 (mpp) REVERT: B 1216 LEU cc_start: 0.8250 (pt) cc_final: 0.7342 (tt) REVERT: B 1323 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7354 (mm) REVERT: C 79 GLU cc_start: 0.8453 (mp0) cc_final: 0.8147 (mp0) outliers start: 55 outliers final: 43 residues processed: 215 average time/residue: 0.1952 time to fit residues: 59.4699 Evaluate side-chains 219 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 906 ASN 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 1051 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 ILE 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: 9.9990 chunk 105 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2828 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= 0.253 Angle : 0.727 18.233 12947 Z= 0.362 Chirality : 0.049 0.269 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.296 47.775 1292 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.24 % Allowed : 33.30 % Favored : 61.46 % 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: -4.66 (0.21), residues: 18 sheet: -1.00 (0.25), residues: 393 loop : -1.53 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.002 TRP B1186 HIS 0.003 0.001 HIS B 947 PHE 0.014 0.001 PHE C 71 TYR 0.018 0.001 TYR B1068 ARG 0.003 0.000 ARG A1977 *********************** 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 224 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 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: A 1994 GLU cc_start: 0.8349 (tt0) cc_final: 0.8113 (tt0) REVERT: A 2032 TYR cc_start: 0.8954 (m-80) cc_final: 0.8641 (m-80) REVERT: A 2036 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 493 LEU cc_start: 0.8633 (tp) cc_final: 0.8225 (tp) REVERT: B 584 MET cc_start: 0.8377 (ptp) cc_final: 0.7950 (ptp) REVERT: B 779 ASP cc_start: 0.7659 (m-30) cc_final: 0.7435 (t0) REVERT: B 993 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: B 998 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7127 (ttp80) REVERT: B 1099 ASP cc_start: 0.7732 (t0) cc_final: 0.7454 (t0) REVERT: B 1127 ASP cc_start: 0.7483 (t0) cc_final: 0.7179 (t0) REVERT: B 1181 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7660 (tmm) REVERT: B 1197 MET cc_start: 0.8767 (mpp) cc_final: 0.7964 (mpp) REVERT: B 1216 LEU cc_start: 0.8278 (pt) cc_final: 0.7368 (tt) REVERT: B 1323 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 79 GLU cc_start: 0.8479 (mp0) cc_final: 0.8168 (mp0) outliers start: 53 outliers final: 47 residues processed: 207 average time/residue: 0.2051 time to fit residues: 60.1660 Evaluate side-chains 218 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG Chi-restraints excluded: chain A residue 1878 PHE Chi-restraints excluded: chain A residue 1919 SER Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 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 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 906 ASN 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 1051 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1068 TYR Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2941 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= 0.284 Angle : 0.727 8.773 12947 Z= 0.367 Chirality : 0.050 0.263 1440 Planarity : 0.005 0.061 1683 Dihedral : 5.444 48.721 1292 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.02 % Rotamer: Outliers : 5.53 % Allowed : 33.10 % Favored : 61.36 % 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: -2.13 (0.24), residues: 1181 helix: -4.67 (0.21), residues: 18 sheet: -1.05 (0.25), residues: 394 loop : -1.58 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.002 TRP B1186 HIS 0.003 0.001 HIS B 947 PHE 0.014 0.001 PHE B 483 TYR 0.024 0.002 TYR B 918 ARG 0.009 0.000 ARG B1170 ********************** 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 fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1994 GLU cc_start: 0.8356 (tt0) cc_final: 0.8133 (tt0) REVERT: A 2036 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 493 LEU cc_start: 0.8628 (tp) cc_final: 0.8128 (tp) REVERT: B 584 MET cc_start: 0.8421 (ptp) cc_final: 0.7996 (ptp) REVERT: B 779 ASP cc_start: 0.7617 (m-30) cc_final: 0.7402 (t0) REVERT: B 883 LYS cc_start: 0.8791 (pttm) cc_final: 0.8191 (pttt) REVERT: B 993 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7236 (t-90) REVERT: B 998 ARG cc_start: 0.7772 (mmt-90) cc_final: 0.7098 (ttp80) REVERT: B 1056 ARG cc_start: 0.8337 (mmm160) cc_final: 0.8093 (mmt-90) REVERT: B 1099 ASP cc_start: 0.7782 (t0) cc_final: 0.7487 (t0) REVERT: B 1127 ASP cc_start: 0.7479 (t0) cc_final: 0.7270 (t0) REVERT: B 1181 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7666 (tmm) REVERT: B 1197 MET cc_start: 0.8804 (mpp) cc_final: 0.7984 (mpp) REVERT: B 1216 LEU cc_start: 0.8290 (pt) cc_final: 0.7352 (tt) REVERT: B 1323 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7500 (mm) REVERT: C 79 GLU cc_start: 0.8475 (mp0) cc_final: 0.8173 (mp0) outliers start: 56 outliers final: 50 residues processed: 207 average time/residue: 0.2003 time to fit residues: 58.8878 Evaluate side-chains 221 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1876 ARG 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 1953 LEU Chi-restraints excluded: chain A residue 1971 ASN Chi-restraints excluded: chain A residue 1975 TRP Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2036 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 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 713 CYS Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 906 ASN 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 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 1101 THR Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1176 HIS Chi-restraints excluded: chain B residue 1178 MET Chi-restraints excluded: chain B residue 1181 MET Chi-restraints excluded: chain B residue 1239 ASP Chi-restraints excluded: chain B residue 1296 LEU Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 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: 1.9990 chunk 85 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.111180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083953 restraints weight = 22499.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087320 restraints weight = 12407.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089711 restraints weight = 8282.907| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3056 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= 0.200 Angle : 0.711 9.596 12947 Z= 0.355 Chirality : 0.049 0.255 1440 Planarity : 0.004 0.061 1683 Dihedral : 5.257 48.275 1292 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.64 % Allowed : 34.19 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.98 (0.24), residues: 1181 helix: -4.65 (0.21), residues: 18 sheet: -0.91 (0.26), residues: 383 loop : -1.49 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.002 TRP B1186 HIS 0.004 0.001 HIS B 947 PHE 0.017 0.001 PHE B 483 TYR 0.019 0.001 TYR B 918 ARG 0.006 0.000 ARG B1170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.42 seconds wall clock time: 39 minutes 13.35 seconds (2353.35 seconds total)