Starting phenix.real_space_refine on Wed Feb 12 02:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjm_31623/02_2025/7fjm_31623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjm_31623/02_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_31623/02_2025/7fjm_31623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjm_31623/02_2025/7fjm_31623.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjm_31623/02_2025/7fjm_31623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjm_31623/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.69, 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: 1.77 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: 0.78 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: 2.11 Time building geometry restraints manager: 2.09 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: 0.980 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.720 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- 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 : 0.685 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: 0.2333 time to fit residues: 38.0052 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 : 0.855 ------------------------------------------------------------------------------- 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 = 0.121997 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: 0.7869 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 : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6224 (tp) REVERT: A 654 LYS cc_start: 0.7381 (mptt) cc_final: 0.7152 (mptt) REVERT: A 686 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8100 (mmm160) REVERT: A 940 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.6398 (p90) REVERT: A 1022 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8545 (tt) outliers start: 26 outliers final: 12 residues processed: 90 average time/residue: 0.1992 time to fit residues: 24.6138 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 : 0.732 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 0.0370 chunk 2 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 40.0000 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.175206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120531 restraints weight = 10077.755| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.14 r_work: 0.3339 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2751 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= 0.186 Angle : 0.660 10.013 9876 Z= 0.324 Chirality : 0.044 0.175 1221 Planarity : 0.006 0.082 1253 Dihedral : 7.105 80.486 1042 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.48 % Favored : 91.20 % Rotamer: Outliers : 4.13 % Allowed : 13.76 % 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: -2.94 (0.25), residues: 955 helix: -1.07 (0.26), residues: 381 sheet: -1.38 (0.49), residues: 86 loop : -2.86 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 306 HIS 0.010 0.001 HIS A 777 PHE 0.017 0.001 PHE A1081 TYR 0.014 0.002 TYR A 240 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 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.751 Fit side-chains REVERT: A 257 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: A 612 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4619 (mm) REVERT: A 654 LYS cc_start: 0.7619 (mptt) cc_final: 0.7263 (mptt) REVERT: A 686 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7829 (mmm160) REVERT: A 744 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7883 (mt) REVERT: A 940 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.6720 (p90) REVERT: A 996 LEU cc_start: 0.8805 (tp) cc_final: 0.8538 (tp) REVERT: A 1009 MET cc_start: 0.8786 (mmm) cc_final: 0.8293 (mmp) REVERT: A 1022 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8689 (tt) outliers start: 30 outliers final: 15 residues processed: 89 average time/residue: 0.1763 time to fit residues: 21.9063 Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.174405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117356 restraints weight = 10148.644| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.57 r_work: 0.3302 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3032 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= 0.156 Angle : 0.628 8.947 9876 Z= 0.305 Chirality : 0.042 0.145 1221 Planarity : 0.006 0.077 1253 Dihedral : 6.775 84.951 1040 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.17 % Favored : 91.52 % Rotamer: Outliers : 4.26 % Allowed : 15.41 % Favored : 80.33 % 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: -2.47 (0.26), residues: 955 helix: -0.58 (0.27), residues: 383 sheet: -1.09 (0.51), residues: 86 loop : -2.71 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.013 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 397 *********************** 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8190 (mtt90) REVERT: A 257 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: A 573 MET cc_start: 0.8022 (mmm) cc_final: 0.7462 (tpp) REVERT: A 612 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4606 (mm) REVERT: A 686 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7783 (mmm160) REVERT: A 744 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 940 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.6944 (p90) REVERT: A 996 LEU cc_start: 0.8771 (tp) cc_final: 0.8514 (tp) REVERT: A 1022 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 1087 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mp) outliers start: 31 outliers final: 15 residues processed: 89 average time/residue: 0.1804 time to fit residues: 22.2614 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 1022 LEU Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1087 LEU 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: 6.9990 chunk 81 optimal weight: 0.9980 chunk 55 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.0060 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.169820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110779 restraints weight = 10071.362| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.24 r_work: 0.3249 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3228 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= 0.248 Angle : 0.679 9.742 9876 Z= 0.329 Chirality : 0.045 0.180 1221 Planarity : 0.006 0.076 1253 Dihedral : 6.816 82.481 1038 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 4.81 % Allowed : 16.09 % 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: -2.30 (0.27), residues: 955 helix: -0.44 (0.27), residues: 383 sheet: -0.90 (0.51), residues: 86 loop : -2.63 (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 0.002 PHE A1081 TYR 0.016 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 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.817 Fit side-chains REVERT: A 257 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: A 523 LEU cc_start: 0.8393 (mt) cc_final: 0.8069 (tp) REVERT: A 612 LEU cc_start: 0.5079 (OUTLIER) cc_final: 0.4630 (mm) REVERT: A 654 LYS cc_start: 0.7559 (mmtm) cc_final: 0.7187 (mptt) REVERT: A 686 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7436 (mmm160) REVERT: A 724 MET cc_start: 0.8480 (mtt) cc_final: 0.7926 (mtm) REVERT: A 940 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.6852 (p90) REVERT: A 1022 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8581 (tt) outliers start: 35 outliers final: 19 residues processed: 91 average time/residue: 0.1918 time to fit residues: 24.6183 Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 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 990 VAL 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: 0.7980 chunk 2 optimal weight: 0.0020 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.5166 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115466 restraints weight = 10150.682| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.57 r_work: 0.3262 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3392 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= 0.160 Angle : 0.636 12.141 9876 Z= 0.305 Chirality : 0.043 0.188 1221 Planarity : 0.006 0.075 1253 Dihedral : 6.574 83.444 1038 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 4.54 % Allowed : 17.47 % 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: -1.96 (0.27), residues: 955 helix: -0.10 (0.28), residues: 383 sheet: -0.61 (0.52), residues: 85 loop : -2.51 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.015 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 199 *********************** 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 94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 435 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6647 (tm) REVERT: A 523 LEU cc_start: 0.8205 (mt) cc_final: 0.7887 (tp) REVERT: A 612 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4572 (mm) REVERT: A 686 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7753 (mmm160) REVERT: A 903 VAL cc_start: 0.8306 (p) cc_final: 0.8070 (p) REVERT: A 940 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7009 (p90) REVERT: A 996 LEU cc_start: 0.8672 (tp) cc_final: 0.8315 (tp) REVERT: A 1022 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8595 (tt) outliers start: 33 outliers final: 19 residues processed: 91 average time/residue: 0.1755 time to fit residues: 22.3682 Evaluate side-chains 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 777 HIS 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 997 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.167164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109209 restraints weight = 10106.892| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.49 r_work: 0.3153 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7225 Z= 0.370 Angle : 0.738 10.831 9876 Z= 0.359 Chirality : 0.047 0.158 1221 Planarity : 0.006 0.075 1253 Dihedral : 6.969 81.854 1038 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.05 % Favored : 89.63 % Rotamer: Outliers : 4.54 % Allowed : 16.78 % Favored : 78.68 % 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: -2.02 (0.27), residues: 955 helix: -0.27 (0.27), residues: 375 sheet: -0.50 (0.53), residues: 82 loop : -2.43 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 258 HIS 0.019 0.001 HIS A 777 PHE 0.024 0.002 PHE A1081 TYR 0.019 0.002 TYR A 259 ARG 0.004 0.001 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 85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.904 Fit side-chains REVERT: A 257 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: A 435 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6595 (tm) REVERT: A 523 LEU cc_start: 0.8200 (mt) cc_final: 0.7833 (tp) REVERT: A 612 LEU cc_start: 0.5133 (OUTLIER) cc_final: 0.4661 (mm) REVERT: A 654 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7123 (mptt) REVERT: A 686 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7894 (mmm160) REVERT: A 940 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7048 (p90) REVERT: A 1022 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8592 (tt) outliers start: 33 outliers final: 21 residues processed: 82 average time/residue: 0.1751 time to fit residues: 20.6748 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 1087 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 48 optimal weight: 40.0000 chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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** A1016 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115205 restraints weight = 10075.416| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.67 r_work: 0.3251 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3661 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= 0.158 Angle : 0.636 10.839 9876 Z= 0.304 Chirality : 0.043 0.172 1221 Planarity : 0.006 0.076 1253 Dihedral : 6.542 84.722 1038 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.99 % Allowed : 17.19 % Favored : 78.82 % 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: -1.69 (0.28), residues: 955 helix: 0.10 (0.28), residues: 382 sheet: -0.48 (0.54), residues: 85 loop : -2.33 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 258 HIS 0.003 0.000 HIS A 413 PHE 0.018 0.001 PHE A 168 TYR 0.010 0.001 TYR A1076 ARG 0.002 0.000 ARG A 199 *********************** 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 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8138 (ptt-90) REVERT: A 257 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: A 348 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5735 (mp0) REVERT: A 435 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6619 (tm) REVERT: A 523 LEU cc_start: 0.8020 (mt) cc_final: 0.7726 (tp) REVERT: A 565 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6592 (pp30) REVERT: A 612 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4638 (mm) REVERT: A 654 LYS cc_start: 0.7505 (mmtm) cc_final: 0.7121 (mptt) REVERT: A 686 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7879 (mmm160) REVERT: A 940 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7100 (p90) REVERT: A 1022 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (tt) outliers start: 29 outliers final: 18 residues processed: 87 average time/residue: 0.1925 time to fit residues: 23.0768 Evaluate side-chains 79 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 916 VAL Chi-restraints excluded: chain A residue 925 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.0050 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.4092 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.174194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116968 restraints weight = 10077.570| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.58 r_work: 0.3294 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7225 Z= 0.150 Angle : 0.625 10.443 9876 Z= 0.297 Chirality : 0.042 0.165 1221 Planarity : 0.005 0.068 1253 Dihedral : 6.288 86.490 1038 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.54 % Favored : 92.15 % Rotamer: Outliers : 3.85 % Allowed : 17.61 % Favored : 78.54 % 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: -1.43 (0.28), residues: 955 helix: 0.37 (0.28), residues: 382 sheet: -0.44 (0.53), residues: 92 loop : -2.25 (0.29), residues: 481 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 0.013 0.001 PHE A1159 TYR 0.010 0.001 TYR A1076 ARG 0.002 0.000 ARG A 199 *********************** 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 97 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: A 316 ASP cc_start: 0.8375 (m-30) cc_final: 0.8102 (t0) REVERT: A 348 GLU cc_start: 0.6178 (mt-10) cc_final: 0.5833 (mp0) REVERT: A 523 LEU cc_start: 0.7958 (mt) cc_final: 0.7692 (tp) REVERT: A 565 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6569 (pp30) REVERT: A 612 LEU cc_start: 0.4976 (OUTLIER) cc_final: 0.4500 (mm) REVERT: A 686 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7835 (mmm160) REVERT: A 940 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7065 (p90) REVERT: A 996 LEU cc_start: 0.8631 (tp) cc_final: 0.8225 (tp) REVERT: A 1022 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8606 (tt) outliers start: 28 outliers final: 20 residues processed: 95 average time/residue: 0.2022 time to fit residues: 26.8587 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 873 VAL 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 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: 50.0000 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 40.0000 chunk 19 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.172669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114477 restraints weight = 10233.384| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.53 r_work: 0.3260 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7225 Z= 0.182 Angle : 0.637 10.222 9876 Z= 0.301 Chirality : 0.043 0.163 1221 Planarity : 0.005 0.065 1253 Dihedral : 6.205 85.249 1036 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.71 % Allowed : 18.16 % Favored : 78.13 % 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: -1.34 (0.28), residues: 955 helix: 0.44 (0.28), residues: 382 sheet: -0.38 (0.54), residues: 92 loop : -2.19 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 306 HIS 0.020 0.001 HIS A 777 PHE 0.023 0.001 PHE A 168 TYR 0.011 0.001 TYR A1076 ARG 0.007 0.000 ARG A 199 ********************** 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 89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 316 ASP cc_start: 0.8410 (m-30) cc_final: 0.8126 (t0) REVERT: A 348 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5776 (mp0) REVERT: A 523 LEU cc_start: 0.8006 (mt) cc_final: 0.7691 (tp) REVERT: A 565 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6554 (pp30) REVERT: A 612 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4417 (mm) REVERT: A 654 LYS cc_start: 0.7487 (mmtm) cc_final: 0.7109 (mptt) REVERT: A 686 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7806 (mmm160) REVERT: A 903 VAL cc_start: 0.8046 (p) cc_final: 0.7810 (p) REVERT: A 940 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7032 (p90) REVERT: A 996 LEU cc_start: 0.8687 (tp) cc_final: 0.8289 (tp) REVERT: A 1022 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8595 (tt) outliers start: 27 outliers final: 21 residues processed: 87 average time/residue: 0.1651 time to fit residues: 20.5017 Evaluate side-chains 84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 873 VAL 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 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 40 optimal weight: 3.9990 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 40.0000 chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 54 optimal weight: 30.0000 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.173871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115283 restraints weight = 10082.183| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.29 r_work: 0.3316 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3943 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= 0.155 Angle : 0.626 10.199 9876 Z= 0.295 Chirality : 0.042 0.159 1221 Planarity : 0.005 0.063 1253 Dihedral : 6.120 84.867 1036 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.43 % Favored : 92.25 % Rotamer: Outliers : 3.85 % Allowed : 18.02 % Favored : 78.13 % 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: -1.23 (0.28), residues: 955 helix: 0.58 (0.28), residues: 382 sheet: -0.34 (0.54), residues: 92 loop : -2.17 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.022 0.001 HIS A 777 PHE 0.013 0.001 PHE A1159 TYR 0.010 0.001 TYR A1076 ARG 0.006 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4664.72 seconds wall clock time: 82 minutes 51.78 seconds (4971.78 seconds total)