Starting phenix.real_space_refine on Wed Mar 12 02:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjm_31623/03_2025/7fjm_31623.cif" } resolution = 3.3 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= 0.008 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 44 5.16 5 C 4566 2.51 5 N 1206 2.21 5 O 1270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7086 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 67, 'TRANS': 905} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 250 Time building chain proxies: 4.67, per 1000 atoms: 0.66 Number of scatterers: 7086 At special positions: 0 Unit cell: (77.9509, 95.5173, 138.335, 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 44 16.00 O 1270 8.00 N 1206 7.00 C 4566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 317 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 42.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 118 through 124 removed outlier: 4.039A pdb=" N GLN A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 124' Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.702A pdb=" N VAL A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS A 198 " --> pdb=" O CYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.786A pdb=" N MET A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.666A pdb=" N VAL A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.679A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.544A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 289 removed outlier: 3.564A pdb=" N SER A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.991A pdb=" N LEU A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 426 through 447 removed outlier: 3.976A pdb=" N TYR A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 451 removed outlier: 3.612A pdb=" N ARG A 451 " --> pdb=" O TYR A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.873A pdb=" N THR A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.714A pdb=" N ILE A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 removed outlier: 3.589A pdb=" N VAL A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.997A pdb=" N TYR A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.752A pdb=" N THR A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 837 removed outlier: 3.801A pdb=" N GLY A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.699A pdb=" N VAL A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 removed outlier: 3.562A pdb=" N LEU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 863 " --> pdb=" O LYS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.572A pdb=" N ALA A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.657A pdb=" N ILE A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 925 " --> pdb=" O ARG A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.518A pdb=" N PHE A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 977 removed outlier: 3.944A pdb=" N PHE A 963 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 981 removed outlier: 4.343A pdb=" N THR A 981 " --> pdb=" O MET A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 998 through 1024 removed outlier: 3.605A pdb=" N VAL A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A1022 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1023 " --> pdb=" O GLY A1019 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1066 removed outlier: 3.665A pdb=" N THR A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A1049 " --> pdb=" O TYR A1045 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1077 Processing helix chain 'A' and resid 1078 through 1098 removed outlier: 3.893A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.695A pdb=" N ALA A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A1108 " --> pdb=" O PRO A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1104 through 1108' Processing helix chain 'A' and resid 1116 through 1121 removed outlier: 3.581A pdb=" N LEU A1121 " --> pdb=" O LYS A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1139 removed outlier: 3.859A pdb=" N ASN A1127 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A1132 " --> pdb=" O PHE A1128 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A1139 " --> pdb=" O GLU A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.704A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 334 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AA3, first strand: chain 'A' and resid 850 through 851 removed outlier: 8.381A pdb=" N PHE A 851 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET A 748 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 510 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 749 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE A 512 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 873 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE A 893 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 530 removed outlier: 3.514A pdb=" N ASP A 524 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 723 " --> pdb=" O MET A 526 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 528 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 721 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 719 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU A 718 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER A 692 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A 720 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 690 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 640 " --> pdb=" O HIS A 626 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS A 626 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA A 642 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 624 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.982A pdb=" N LEU A 564 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 792 through 793 removed outlier: 6.768A pdb=" N HIS A 772 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA A 824 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 774 " --> pdb=" O ALA A 824 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 696 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: 2.18 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1006 1.24 - 1.38: 1625 1.38 - 1.52: 3324 1.52 - 1.67: 1205 1.67 - 1.81: 65 Bond restraints: 7225 Sorted by residual: bond pdb=" CA ALA A 965 " pdb=" C ALA A 965 " ideal model delta sigma weight residual 1.524 1.331 0.193 1.27e-02 6.20e+03 2.31e+02 bond pdb=" CA ILE A 966 " pdb=" C ILE A 966 " ideal model delta sigma weight residual 1.524 1.385 0.139 1.18e-02 7.18e+03 1.39e+02 bond pdb=" C LEU A 961 " pdb=" O LEU A 961 " ideal model delta sigma weight residual 1.236 1.098 0.137 1.29e-02 6.01e+03 1.13e+02 bond pdb=" C SER A1052 " pdb=" O SER A1052 " ideal model delta sigma weight residual 1.236 1.357 -0.120 1.15e-02 7.56e+03 1.09e+02 bond pdb=" CA SER A 904 " pdb=" C SER A 904 " ideal model delta sigma weight residual 1.524 1.394 0.129 1.26e-02 6.30e+03 1.06e+02 ... (remaining 7220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 9661 4.88 - 9.76: 197 9.76 - 14.64: 15 14.64 - 19.53: 2 19.53 - 24.41: 1 Bond angle restraints: 9876 Sorted by residual: angle pdb=" C SER A 904 " pdb=" N PRO A 905 " pdb=" CA PRO A 905 " ideal model delta sigma weight residual 119.84 102.41 17.43 1.25e+00 6.40e-01 1.95e+02 angle pdb=" N SER A 904 " pdb=" CA SER A 904 " pdb=" C SER A 904 " ideal model delta sigma weight residual 109.81 85.40 24.41 2.21e+00 2.05e-01 1.22e+02 angle pdb=" N LEU A 432 " pdb=" CA LEU A 432 " pdb=" C LEU A 432 " ideal model delta sigma weight residual 111.28 101.41 9.87 1.09e+00 8.42e-01 8.20e+01 angle pdb=" N LEU A 64 " pdb=" CA LEU A 64 " pdb=" C LEU A 64 " ideal model delta sigma weight residual 113.16 102.25 10.91 1.24e+00 6.50e-01 7.74e+01 angle pdb=" N MET A 426 " pdb=" CA MET A 426 " pdb=" C MET A 426 " ideal model delta sigma weight residual 114.75 103.67 11.08 1.26e+00 6.30e-01 7.73e+01 ... (remaining 9871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 4000 15.61 - 31.22: 253 31.22 - 46.83: 69 46.83 - 62.44: 20 62.44 - 78.05: 2 Dihedral angle restraints: 4344 sinusoidal: 1538 harmonic: 2806 Sorted by residual: dihedral pdb=" C GLN A 944 " pdb=" N GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual -122.60 -143.40 20.80 0 2.50e+00 1.60e-01 6.92e+01 dihedral pdb=" N ILE A 946 " pdb=" C ILE A 946 " pdb=" CA ILE A 946 " pdb=" CB ILE A 946 " ideal model delta harmonic sigma weight residual 123.40 143.97 -20.57 0 2.50e+00 1.60e-01 6.77e+01 dihedral pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CA GLN A 944 " pdb=" CB GLN A 944 " ideal model delta harmonic sigma weight residual 122.80 143.33 -20.53 0 2.50e+00 1.60e-01 6.75e+01 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1130 0.197 - 0.393: 61 0.393 - 0.590: 25 0.590 - 0.786: 3 0.786 - 0.983: 2 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CA GLN A 944 " pdb=" N GLN A 944 " pdb=" C GLN A 944 " pdb=" CB GLN A 944 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ILE A 946 " pdb=" N ILE A 946 " pdb=" C ILE A 946 " pdb=" CB ILE A 946 " both_signs ideal model delta sigma weight residual False 2.43 1.61 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CA PHE A 906 " pdb=" N PHE A 906 " pdb=" C PHE A 906 " pdb=" CB PHE A 906 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 1218 not shown) Planarity restraints: 1253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 967 " 0.039 2.00e-02 2.50e+03 7.51e-02 5.64e+01 pdb=" C ASP A 967 " -0.130 2.00e-02 2.50e+03 pdb=" O ASP A 967 " 0.047 2.00e-02 2.50e+03 pdb=" N LEU A 968 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 966 " 0.038 2.00e-02 2.50e+03 7.14e-02 5.10e+01 pdb=" C ILE A 966 " -0.124 2.00e-02 2.50e+03 pdb=" O ILE A 966 " 0.044 2.00e-02 2.50e+03 pdb=" N ASP A 967 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 969 " 0.037 2.00e-02 2.50e+03 7.04e-02 4.95e+01 pdb=" C VAL A 969 " -0.122 2.00e-02 2.50e+03 pdb=" O VAL A 969 " 0.044 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.040 2.00e-02 2.50e+03 ... (remaining 1250 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 716 2.73 - 3.28: 6698 3.28 - 3.82: 10860 3.82 - 4.36: 13093 4.36 - 4.90: 22003 Nonbonded interactions: 53370 Sorted by model distance: nonbonded pdb=" N VAL A 903 " pdb=" O VAL A 903 " model vdw 2.194 2.496 nonbonded pdb=" O SER A 904 " pdb=" CA PRO A 905 " model vdw 2.280 2.776 nonbonded pdb=" N SER A 908 " pdb=" O SER A 908 " model vdw 2.322 2.496 nonbonded pdb=" O ALA A 965 " pdb=" O ILE A 966 " model vdw 2.349 3.040 nonbonded pdb=" N SER A1055 " pdb=" OG SER A1055 " model vdw 2.369 2.496 ... (remaining 53365 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 individual isotropic 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.380 Find NCS groups from input model: 0.070 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.014 0.193 7225 Z= 0.952 Angle : 1.571 24.407 9876 Z= 0.989 Chirality : 0.121 0.983 1221 Planarity : 0.012 0.142 1253 Dihedral : 11.982 78.054 2525 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.21 % Favored : 90.26 % Rotamer: Outliers : 3.44 % Allowed : 9.63 % Favored : 86.93 % Cbeta Deviations : 1.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.28 (0.23), residues: 955 helix: -2.66 (0.24), residues: 361 sheet: -2.09 (0.48), residues: 86 loop : -3.19 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.014 0.001 HIS A 497 PHE 0.043 0.003 PHE A 945 TYR 0.040 0.003 TYR A 940 ARG 0.005 0.001 ARG A 980 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.8172 (mmm) cc_final: 0.7958 (mmt) REVERT: A 937 MET cc_start: 0.8134 (mmt) cc_final: 0.7796 (mmt) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.2252 time to fit residues: 36.7117 Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1057 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN A1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121991 restraints weight = 10237.217| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.87 r_work: 0.3360 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7225 Z= 0.183 Angle : 0.706 11.251 9876 Z= 0.350 Chirality : 0.045 0.336 1221 Planarity : 0.007 0.079 1253 Dihedral : 8.154 78.190 1052 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.80 % Favored : 90.89 % Rotamer: Outliers : 3.58 % Allowed : 12.79 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -3.65 (0.24), residues: 955 helix: -1.88 (0.24), residues: 375 sheet: -2.08 (0.46), residues: 96 loop : -2.98 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 258 HIS 0.007 0.001 HIS A 497 PHE 0.015 0.001 PHE A1081 TYR 0.022 0.002 TYR A 240 ARG 0.004 0.001 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6227 (tp) REVERT: A 654 LYS cc_start: 0.7396 (mptt) cc_final: 0.7165 (mptt) REVERT: A 686 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8107 (mmm160) REVERT: A 940 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6400 (p90) REVERT: A 1022 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8545 (tt) outliers start: 26 outliers final: 12 residues processed: 90 average time/residue: 0.1889 time to fit residues: 23.5124 Evaluate side-chains 69 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS A1008 GLN A1127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.175343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127922 restraints weight = 10072.521| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.72 r_work: 0.3396 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7225 Z= 0.184 Angle : 0.659 10.009 9876 Z= 0.324 Chirality : 0.044 0.176 1221 Planarity : 0.006 0.081 1253 Dihedral : 7.127 80.225 1042 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.48 % Favored : 91.20 % Rotamer: Outliers : 4.40 % Allowed : 13.48 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.96 (0.25), residues: 955 helix: -1.10 (0.26), residues: 381 sheet: -1.37 (0.49), residues: 86 loop : -2.87 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 306 HIS 0.009 0.001 HIS A 777 PHE 0.016 0.001 PHE A1081 TYR 0.014 0.002 TYR A1076 ARG 0.003 0.000 ARG A 921 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.784 Fit side-chains REVERT: A 257 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: A 612 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4619 (mm) REVERT: A 654 LYS cc_start: 0.7645 (mptt) cc_final: 0.7303 (mptt) REVERT: A 686 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7808 (mmm160) REVERT: A 744 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7881 (mt) REVERT: A 940 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.6634 (p90) REVERT: A 961 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 996 LEU cc_start: 0.8747 (tp) cc_final: 0.8478 (tp) REVERT: A 1009 MET cc_start: 0.8699 (mmm) cc_final: 0.8155 (mmp) REVERT: A 1022 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8669 (tt) outliers start: 32 outliers final: 15 residues processed: 90 average time/residue: 0.1699 time to fit residues: 21.3798 Evaluate side-chains 79 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 777 HIS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 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 = 0.4169 r_free = 0.4169 target = 0.173388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116692 restraints weight = 10163.796| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.75 r_work: 0.3263 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7225 Z= 0.178 Angle : 0.638 9.013 9876 Z= 0.310 Chirality : 0.043 0.141 1221 Planarity : 0.006 0.077 1253 Dihedral : 6.975 84.490 1042 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.80 % Favored : 90.89 % Rotamer: Outliers : 4.40 % Allowed : 15.54 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.51 (0.26), residues: 955 helix: -0.63 (0.27), residues: 382 sheet: -1.10 (0.51), residues: 86 loop : -2.71 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.015 0.001 HIS A 777 PHE 0.017 0.001 PHE A 168 TYR 0.013 0.001 TYR A1076 ARG 0.002 0.000 ARG A 921 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: A 573 MET cc_start: 0.8038 (mmm) cc_final: 0.7484 (tpp) REVERT: A 612 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4574 (mm) REVERT: A 686 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7753 (mmm160) REVERT: A 744 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 940 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 996 LEU cc_start: 0.8735 (tp) cc_final: 0.8454 (tp) REVERT: A 1011 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 1022 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 1087 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8093 (mp) outliers start: 32 outliers final: 17 residues processed: 88 average time/residue: 0.1853 time to fit residues: 22.3868 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 55 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113483 restraints weight = 10075.720| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.57 r_work: 0.3195 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7225 Z= 0.251 Angle : 0.679 9.751 9876 Z= 0.330 Chirality : 0.045 0.189 1221 Planarity : 0.006 0.077 1253 Dihedral : 6.929 82.125 1040 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.11 % Favored : 90.58 % Rotamer: Outliers : 4.68 % Allowed : 16.23 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.27), residues: 955 helix: -0.47 (0.27), residues: 383 sheet: -0.93 (0.51), residues: 86 loop : -2.64 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.012 0.001 HIS A 777 PHE 0.019 0.001 PHE A1081 TYR 0.015 0.002 TYR A1045 ARG 0.003 0.000 ARG A 921 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.868 Fit side-chains REVERT: A 257 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: A 523 LEU cc_start: 0.8391 (mt) cc_final: 0.8090 (tp) REVERT: A 612 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4657 (mm) REVERT: A 654 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7112 (mptt) REVERT: A 686 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7655 (mmm160) REVERT: A 940 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.6767 (p90) REVERT: A 978 MET cc_start: 0.9050 (ttp) cc_final: 0.8798 (ttm) REVERT: A 1022 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8561 (tt) outliers start: 34 outliers final: 20 residues processed: 90 average time/residue: 0.1724 time to fit residues: 21.8619 Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 HIS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 19 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.172731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115585 restraints weight = 10159.967| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.67 r_work: 0.3259 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7225 Z= 0.161 Angle : 0.630 12.104 9876 Z= 0.302 Chirality : 0.042 0.146 1221 Planarity : 0.005 0.076 1253 Dihedral : 6.575 83.569 1038 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % Rotamer: Outliers : 4.13 % Allowed : 17.61 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.96 (0.27), residues: 955 helix: -0.11 (0.28), residues: 383 sheet: -0.65 (0.52), residues: 85 loop : -2.51 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.016 0.001 HIS A 777 PHE 0.020 0.001 PHE A 168 TYR 0.012 0.001 TYR A1076 ARG 0.002 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: A 435 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6679 (tm) REVERT: A 523 LEU cc_start: 0.8058 (mt) cc_final: 0.7806 (tp) REVERT: A 612 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4672 (mm) REVERT: A 654 LYS cc_start: 0.7674 (mmtm) cc_final: 0.7213 (mptt) REVERT: A 686 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7721 (mmm160) REVERT: A 903 VAL cc_start: 0.8309 (p) cc_final: 0.8087 (p) REVERT: A 940 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7008 (p90) REVERT: A 978 MET cc_start: 0.9061 (ttp) cc_final: 0.8847 (ttm) REVERT: A 996 LEU cc_start: 0.8650 (tp) cc_final: 0.8293 (tp) REVERT: A 1022 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8579 (tt) outliers start: 30 outliers final: 15 residues processed: 87 average time/residue: 0.1666 time to fit residues: 20.7569 Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS A1016 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.167161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108927 restraints weight = 10025.582| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.47 r_work: 0.3162 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7225 Z= 0.332 Angle : 0.716 10.448 9876 Z= 0.348 Chirality : 0.046 0.150 1221 Planarity : 0.006 0.075 1253 Dihedral : 6.930 80.834 1038 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.26 % Favored : 89.42 % Rotamer: Outliers : 4.81 % Allowed : 17.06 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.27), residues: 955 helix: -0.24 (0.27), residues: 375 sheet: -0.54 (0.53), residues: 82 loop : -2.44 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 258 HIS 0.014 0.001 HIS A 777 PHE 0.022 0.002 PHE A1081 TYR 0.018 0.002 TYR A 259 ARG 0.004 0.000 ARG A1073 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 53 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: A 435 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6605 (tm) REVERT: A 523 LEU cc_start: 0.8172 (mt) cc_final: 0.7866 (tp) REVERT: A 612 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4634 (mm) REVERT: A 654 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7215 (mptt) REVERT: A 686 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7829 (mmm160) REVERT: A 940 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7010 (p90) REVERT: A 1022 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 35 outliers final: 23 residues processed: 85 average time/residue: 0.1520 time to fit residues: 18.9436 Evaluate side-chains 79 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 777 HIS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113225 restraints weight = 10068.926| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.79 r_work: 0.3236 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7225 Z= 0.174 Angle : 0.642 10.768 9876 Z= 0.309 Chirality : 0.044 0.191 1221 Planarity : 0.006 0.073 1253 Dihedral : 6.590 83.202 1038 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.85 % Allowed : 17.74 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.28), residues: 955 helix: 0.07 (0.28), residues: 382 sheet: -0.54 (0.53), residues: 85 loop : -2.37 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 HIS 0.020 0.001 HIS A 777 PHE 0.020 0.001 PHE A 168 TYR 0.011 0.001 TYR A1076 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: A 435 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6568 (tm) REVERT: A 523 LEU cc_start: 0.8135 (mt) cc_final: 0.7827 (tp) REVERT: A 565 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6607 (pp30) REVERT: A 612 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4635 (mm) REVERT: A 686 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7960 (mmm160) REVERT: A 940 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7126 (p90) REVERT: A 1022 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (tt) outliers start: 28 outliers final: 19 residues processed: 86 average time/residue: 0.1857 time to fit residues: 22.5511 Evaluate side-chains 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 777 HIS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 88 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 46 optimal weight: 0.4980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS A1016 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.174368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117443 restraints weight = 10116.433| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.67 r_work: 0.3295 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7225 Z= 0.145 Angle : 0.624 10.744 9876 Z= 0.298 Chirality : 0.042 0.168 1221 Planarity : 0.005 0.067 1253 Dihedral : 6.317 86.414 1038 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.58 % Allowed : 18.43 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.28), residues: 955 helix: 0.37 (0.28), residues: 382 sheet: -0.42 (0.54), residues: 85 loop : -2.30 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.024 0.001 HIS A 777 PHE 0.016 0.001 PHE A1128 TYR 0.010 0.001 TYR A1076 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: A 348 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5855 (mp0) REVERT: A 435 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6797 (tm) REVERT: A 523 LEU cc_start: 0.8143 (mt) cc_final: 0.7864 (tp) REVERT: A 565 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6572 (pp30) REVERT: A 612 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4526 (mm) REVERT: A 654 LYS cc_start: 0.7475 (mmtm) cc_final: 0.7118 (mptt) REVERT: A 686 ARG cc_start: 0.8343 (mmm160) cc_final: 0.7948 (mmm160) REVERT: A 940 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7058 (p90) REVERT: A 1022 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8607 (tt) outliers start: 26 outliers final: 19 residues processed: 86 average time/residue: 0.1852 time to fit residues: 22.2912 Evaluate side-chains 79 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 777 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 0 optimal weight: 40.0000 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.173815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118709 restraints weight = 10277.438| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.74 r_work: 0.3272 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7225 Z= 0.158 Angle : 0.621 10.364 9876 Z= 0.296 Chirality : 0.043 0.170 1221 Planarity : 0.005 0.064 1253 Dihedral : 6.305 87.007 1038 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.12 % Favored : 92.57 % Rotamer: Outliers : 3.58 % Allowed : 18.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.28), residues: 955 helix: 0.50 (0.28), residues: 382 sheet: -0.42 (0.53), residues: 92 loop : -2.18 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 306 HIS 0.019 0.001 HIS A 777 PHE 0.023 0.001 PHE A 168 TYR 0.010 0.001 TYR A1076 ARG 0.004 0.000 ARG A 821 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: A 316 ASP cc_start: 0.8291 (m-30) cc_final: 0.7990 (t0) REVERT: A 523 LEU cc_start: 0.8184 (mt) cc_final: 0.7863 (tp) REVERT: A 565 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6560 (pp30) REVERT: A 612 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4471 (mm) REVERT: A 654 LYS cc_start: 0.7487 (mmtm) cc_final: 0.7142 (mptt) REVERT: A 686 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7870 (mmm160) REVERT: A 940 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.6980 (p90) REVERT: A 996 LEU cc_start: 0.8642 (tp) cc_final: 0.8257 (tp) REVERT: A 1022 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (tt) outliers start: 26 outliers final: 18 residues processed: 86 average time/residue: 0.1833 time to fit residues: 22.1078 Evaluate side-chains 80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 4.9990 chunk 91 optimal weight: 0.0020 chunk 55 optimal weight: 40.0000 chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 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 = 0.4177 r_free = 0.4177 target = 0.174188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117931 restraints weight = 10109.436| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.60 r_work: 0.3276 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7225 Z= 0.160 Angle : 0.633 10.129 9876 Z= 0.301 Chirality : 0.043 0.170 1221 Planarity : 0.005 0.059 1253 Dihedral : 6.112 85.294 1036 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.54 % Favored : 92.15 % Rotamer: Outliers : 3.58 % Allowed : 18.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.28), residues: 955 helix: 0.59 (0.28), residues: 383 sheet: -0.45 (0.53), residues: 89 loop : -2.18 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 306 HIS 0.002 0.000 HIS A 413 PHE 0.017 0.001 PHE A1128 TYR 0.010 0.001 TYR A1076 ARG 0.002 0.000 ARG A 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.75 seconds wall clock time: 74 minutes 57.80 seconds (4497.80 seconds total)