Starting phenix.real_space_refine on Sat Dec 28 00:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjm_31623/12_2024/7fjm_31623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjm_31623/12_2024/7fjm_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_31623/12_2024/7fjm_31623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjm_31623/12_2024/7fjm_31623.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjm_31623/12_2024/7fjm_31623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjm_31623/12_2024/7fjm_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-5532/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: 4.72, per 1000 atoms: 0.67 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: 1.67 Conformation dependent library (CDL) restraints added in 1.2 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: 0.85 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: 2.01 Time building geometry restraints manager: 1.94 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: 0.640 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.970 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:2.920 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 : 0.699 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: 0.2351 time to fit residues: 38.3297 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 : 0.713 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 937 MET cc_start: 0.7917 (mmt) cc_final: 0.7712 (mmt) REVERT: A 940 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.6272 (p90) outliers start: 26 outliers final: 12 residues processed: 90 average time/residue: 0.1958 time to fit residues: 24.2694 Evaluate side-chains 66 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 48 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 0.0370 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7225 Z= 0.181 Angle : 0.663 10.165 9876 Z= 0.324 Chirality : 0.044 0.172 1221 Planarity : 0.006 0.081 1253 Dihedral : 7.105 80.436 1042 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.27 % Favored : 91.41 % Rotamer: Outliers : 3.99 % Allowed : 13.76 % Favored : 82.26 % 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: -2.95 (0.25), residues: 955 helix: -1.05 (0.26), residues: 381 sheet: -1.46 (0.47), residues: 87 loop : -2.88 (0.26), residues: 487 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 0.015 0.002 TYR A1076 ARG 0.003 0.000 ARG A 725 *********************** 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 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.794 Fit side-chains REVERT: A 257 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: A 612 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4244 (mm) REVERT: A 744 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 937 MET cc_start: 0.7874 (mmt) cc_final: 0.7636 (mmt) REVERT: A 940 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.6449 (p90) REVERT: A 996 LEU cc_start: 0.8455 (tp) cc_final: 0.8254 (tp) outliers start: 29 outliers final: 15 residues processed: 88 average time/residue: 0.1835 time to fit residues: 22.6173 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 87 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7225 Z= 0.147 Angle : 0.626 9.016 9876 Z= 0.303 Chirality : 0.042 0.141 1221 Planarity : 0.006 0.076 1253 Dihedral : 6.738 85.097 1040 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % Rotamer: Outliers : 3.71 % Allowed : 16.23 % 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: -2.42 (0.26), residues: 955 helix: -0.54 (0.27), residues: 382 sheet: -1.07 (0.50), residues: 86 loop : -2.67 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.012 0.001 HIS A 777 PHE 0.016 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 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: A 573 MET cc_start: 0.6362 (mmm) cc_final: 0.6011 (tpp) REVERT: A 612 LEU cc_start: 0.4632 (OUTLIER) cc_final: 0.4164 (mm) REVERT: A 903 VAL cc_start: 0.7715 (p) cc_final: 0.7506 (p) REVERT: A 940 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.6611 (p90) REVERT: A 961 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 1087 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7972 (mp) outliers start: 27 outliers final: 14 residues processed: 84 average time/residue: 0.1838 time to fit residues: 21.6244 Evaluate side-chains 72 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 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 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 552 LEU Chi-restraints excluded: chain A residue 612 LEU 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 990 VAL Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1092 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7225 Z= 0.218 Angle : 0.645 8.936 9876 Z= 0.314 Chirality : 0.044 0.143 1221 Planarity : 0.006 0.075 1253 Dihedral : 6.640 83.016 1038 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.80 % Favored : 90.89 % Rotamer: Outliers : 4.95 % Allowed : 16.09 % Favored : 78.95 % 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: -2.19 (0.27), residues: 955 helix: -0.34 (0.27), residues: 383 sheet: -0.84 (0.51), residues: 86 loop : -2.59 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.013 0.001 HIS A 777 PHE 0.017 0.001 PHE A1081 TYR 0.014 0.002 TYR A1076 ARG 0.003 0.000 ARG A1073 *********************** 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: 36 poor density : 59 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: A 612 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4173 (mm) REVERT: A 903 VAL cc_start: 0.7714 (p) cc_final: 0.7514 (p) REVERT: A 940 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.6653 (p90) outliers start: 36 outliers final: 20 residues processed: 90 average time/residue: 0.1933 time to fit residues: 23.8958 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 552 LEU Chi-restraints excluded: chain A residue 612 LEU 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 940 TYR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL 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 31 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 40.0000 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7225 Z= 0.194 Angle : 0.641 11.816 9876 Z= 0.310 Chirality : 0.043 0.191 1221 Planarity : 0.006 0.074 1253 Dihedral : 6.567 82.690 1038 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.27 % Favored : 91.41 % Rotamer: Outliers : 4.26 % Allowed : 17.47 % Favored : 78.27 % 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: -1.97 (0.27), residues: 955 helix: -0.15 (0.27), residues: 383 sheet: -0.62 (0.52), residues: 85 loop : -2.49 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.016 0.001 HIS A 777 PHE 0.019 0.001 PHE A 168 TYR 0.013 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 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: A 435 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7296 (tm) REVERT: A 612 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.4160 (mm) REVERT: A 940 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6595 (p90) outliers start: 31 outliers final: 18 residues processed: 88 average time/residue: 0.1825 time to fit residues: 22.7621 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 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 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL 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 10 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7225 Z= 0.219 Angle : 0.660 10.858 9876 Z= 0.318 Chirality : 0.044 0.170 1221 Planarity : 0.006 0.076 1253 Dihedral : 6.574 82.645 1038 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.59 % Favored : 91.10 % Rotamer: Outliers : 3.99 % Allowed : 17.06 % Favored : 78.95 % 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: -1.89 (0.27), residues: 955 helix: -0.07 (0.28), residues: 382 sheet: -0.60 (0.51), residues: 85 loop : -2.45 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.016 0.001 HIS A 777 PHE 0.014 0.001 PHE A1081 TYR 0.012 0.001 TYR A1076 ARG 0.002 0.000 ARG A 921 *********************** 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: 29 poor density : 56 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: A 435 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7336 (tm) REVERT: A 612 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4127 (mm) REVERT: A 940 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.6618 (p90) outliers start: 29 outliers final: 19 residues processed: 84 average time/residue: 0.1766 time to fit residues: 20.8270 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 612 LEU Chi-restraints excluded: chain A residue 722 LEU 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 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3698 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= 0.162 Angle : 0.632 10.688 9876 Z= 0.305 Chirality : 0.042 0.151 1221 Planarity : 0.005 0.067 1253 Dihedral : 6.369 83.620 1038 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.33 % Favored : 92.36 % Rotamer: Outliers : 3.71 % Allowed : 17.61 % Favored : 78.68 % 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: -1.66 (0.28), residues: 955 helix: 0.15 (0.28), residues: 382 sheet: -0.52 (0.52), residues: 85 loop : -2.33 (0.28), residues: 488 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 0.011 0.001 TYR A1076 ARG 0.004 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 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: A 435 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7336 (tm) REVERT: A 612 LEU cc_start: 0.4612 (OUTLIER) cc_final: 0.4146 (mm) REVERT: A 940 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.6747 (p90) outliers start: 27 outliers final: 19 residues processed: 86 average time/residue: 0.1839 time to fit residues: 22.0790 Evaluate side-chains 74 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 612 LEU Chi-restraints excluded: chain A residue 722 LEU 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 1057 GLN Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7225 Z= 0.182 Angle : 0.646 10.391 9876 Z= 0.311 Chirality : 0.043 0.154 1221 Planarity : 0.006 0.068 1253 Dihedral : 6.368 83.512 1038 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.75 % Favored : 91.94 % Rotamer: Outliers : 3.99 % Allowed : 18.02 % 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: -1.63 (0.28), residues: 955 helix: 0.26 (0.28), residues: 382 sheet: -0.57 (0.51), residues: 86 loop : -2.37 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 306 HIS 0.018 0.001 HIS A 777 PHE 0.014 0.001 PHE A1159 TYR 0.011 0.001 TYR A1076 ARG 0.004 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 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: A 435 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7358 (tm) REVERT: A 612 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4139 (mm) REVERT: A 903 VAL cc_start: 0.7534 (p) cc_final: 0.7310 (p) REVERT: A 940 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.6653 (p90) outliers start: 29 outliers final: 21 residues processed: 81 average time/residue: 0.1761 time to fit residues: 20.3089 Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 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 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 996 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 47 optimal weight: 40.0000 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7225 Z= 0.180 Angle : 0.647 11.665 9876 Z= 0.311 Chirality : 0.043 0.212 1221 Planarity : 0.006 0.068 1253 Dihedral : 6.335 83.098 1038 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 3.71 % Allowed : 18.02 % 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: -1.57 (0.28), residues: 955 helix: 0.32 (0.28), residues: 382 sheet: -0.56 (0.52), residues: 86 loop : -2.35 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 306 HIS 0.019 0.001 HIS A 777 PHE 0.023 0.001 PHE A 168 TYR 0.011 0.001 TYR A1076 ARG 0.003 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 83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 257 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: A 435 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7404 (tm) REVERT: A 612 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4071 (mm) REVERT: A 903 VAL cc_start: 0.7547 (p) cc_final: 0.7321 (p) REVERT: A 940 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.6697 (p90) outliers start: 27 outliers final: 21 residues processed: 83 average time/residue: 0.1790 time to fit residues: 20.8451 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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 963 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 990 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.0040 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.173194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115869 restraints weight = 9926.471| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.61 r_work: 0.3280 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 7225 Z= 0.366 Angle : 1.033 59.199 9876 Z= 0.584 Chirality : 0.059 1.077 1221 Planarity : 0.007 0.152 1253 Dihedral : 6.326 83.111 1038 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.33 % Favored : 92.36 % Rotamer: Outliers : 3.71 % Allowed : 17.74 % Favored : 78.54 % Cbeta Deviations : 0.22 % 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: -1.56 (0.28), residues: 955 helix: 0.33 (0.28), residues: 382 sheet: -0.55 (0.52), residues: 86 loop : -2.35 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 306 HIS 0.200 0.008 HIS A 777 PHE 0.016 0.001 PHE A 168 TYR 0.011 0.001 TYR A1076 ARG 0.006 0.000 ARG A 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.83 seconds wall clock time: 32 minutes 21.13 seconds (1941.13 seconds total)