Starting phenix.real_space_refine on Fri Mar 14 04:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2025/7zk4_14754.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 6028 2.51 5 N 1554 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9337 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9094 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 29, 'TRANS': 1146} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 243 Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 5} Classifications: {'undetermined': 9, 'water': 4} Link IDs: {None: 12} Time building chain proxies: 6.12, per 1000 atoms: 0.66 Number of scatterers: 9337 At special positions: 0 Unit cell: (71.982, 87.048, 148.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 6 15.00 Mg 2 11.99 O 1716 8.00 N 1554 7.00 C 6028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 42 through 69 removed outlier: 3.805A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.524A pdb=" N VAL A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 154 removed outlier: 6.143A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 180 removed outlier: 4.216A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 3.854A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.508A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 319 Processing helix chain 'A' and resid 323 through 344 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.756A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.946A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.511A pdb=" N GLN A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.752A pdb=" N THR A 518 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.700A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.567A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.503A pdb=" N LYS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.678A pdb=" N ASN A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.073A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 795 removed outlier: 3.548A pdb=" N PHE A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.534A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.932A pdb=" N ALA A 824 " --> pdb=" O GLN A 820 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.820A pdb=" N GLY A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 899 removed outlier: 4.077A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.871A pdb=" N GLU A 871 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 920 through 962 removed outlier: 3.706A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 982 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 990 through 1009 removed outlier: 3.522A pdb=" N LYS A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.631A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 removed outlier: 3.525A pdb=" N THR A1170 " --> pdb=" O ASP A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 3.976A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 Processing helix chain 'A' and resid 1229 through 1233 Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.512A pdb=" N GLN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1269 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.789A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.489A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 598 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056 removed outlier: 6.881A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A1036 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A1087 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.384A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1851 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: 3.33 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1509 1.28 - 1.42: 2367 1.42 - 1.55: 5560 1.55 - 1.69: 21 1.69 - 1.82: 61 Bond restraints: 9518 Sorted by residual: bond pdb=" C LEU A 48 " pdb=" O LEU A 48 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.29e-02 6.01e+03 4.89e+01 bond pdb=" C HIS A 932 " pdb=" O HIS A 932 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.37e+01 bond pdb=" C MET A 928 " pdb=" O MET A 928 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.26e-02 6.30e+03 3.99e+01 bond pdb=" C LEU A 134 " pdb=" O LEU A 134 " ideal model delta sigma weight residual 1.237 1.166 0.070 1.19e-02 7.06e+03 3.47e+01 bond pdb=" CA ALA A 943 " pdb=" CB ALA A 943 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.59e-02 3.96e+03 2.84e+01 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 12706 3.06 - 6.11: 184 6.11 - 9.17: 18 9.17 - 12.22: 3 12.22 - 15.28: 2 Bond angle restraints: 12913 Sorted by residual: angle pdb=" N ILE A 127 " pdb=" CA ILE A 127 " pdb=" C ILE A 127 " ideal model delta sigma weight residual 111.00 101.28 9.72 1.09e+00 8.42e-01 7.95e+01 angle pdb=" N SER A 88 " pdb=" CA SER A 88 " pdb=" C SER A 88 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N MET A 91 " pdb=" CA MET A 91 " pdb=" C MET A 91 " ideal model delta sigma weight residual 111.54 101.60 9.94 1.36e+00 5.41e-01 5.34e+01 angle pdb=" O2B ATP A2001 " pdb=" PB ATP A2001 " pdb=" O3B ATP A2001 " ideal model delta sigma weight residual 106.94 119.22 -12.28 1.88e+00 2.83e-01 4.27e+01 angle pdb=" C ARG A 954 " pdb=" CA ARG A 954 " pdb=" CB ARG A 954 " ideal model delta sigma weight residual 110.85 100.62 10.23 1.70e+00 3.46e-01 3.62e+01 ... (remaining 12908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5554 23.49 - 46.98: 305 46.98 - 70.47: 54 70.47 - 93.96: 19 93.96 - 117.44: 3 Dihedral angle restraints: 5935 sinusoidal: 2567 harmonic: 3368 Sorted by residual: dihedral pdb=" C ARG A 954 " pdb=" N ARG A 954 " pdb=" CA ARG A 954 " pdb=" CB ARG A 954 " ideal model delta harmonic sigma weight residual -122.60 -107.79 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" C ILE A 860 " pdb=" N ILE A 860 " pdb=" CA ILE A 860 " pdb=" CB ILE A 860 " ideal model delta harmonic sigma weight residual -122.00 -134.06 12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C TYR A 946 " pdb=" N TYR A 946 " pdb=" CA TYR A 946 " pdb=" CB TYR A 946 " ideal model delta harmonic sigma weight residual -122.60 -134.22 11.62 0 2.50e+00 1.60e-01 2.16e+01 ... (remaining 5932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1328 0.075 - 0.151: 134 0.151 - 0.226: 18 0.226 - 0.302: 6 0.302 - 0.377: 4 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA TYR A 946 " pdb=" N TYR A 946 " pdb=" C TYR A 946 " pdb=" CB TYR A 946 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA ARG A 954 " pdb=" N ARG A 954 " pdb=" C ARG A 954 " pdb=" CB ARG A 954 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE A 860 " pdb=" N ILE A 860 " pdb=" C ILE A 860 " pdb=" CB ILE A 860 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1487 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 858 " -0.023 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU A 858 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU A 858 " -0.030 2.00e-02 2.50e+03 pdb=" N ALA A 859 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 860 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ILE A 860 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE A 860 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL A 861 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 79 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ALA A 79 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 79 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 80 " -0.022 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 73 2.59 - 3.16: 8192 3.16 - 3.74: 15320 3.74 - 4.32: 21459 4.32 - 4.90: 34768 Nonbonded interactions: 79812 Sorted by model distance: nonbonded pdb=" OG SER A 430 " pdb="MG MG A2002 " model vdw 2.008 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2102 " model vdw 2.053 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2101 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2103 " model vdw 2.063 2.170 nonbonded pdb=" OG SER A1073 " pdb="MG MG A2004 " model vdw 2.076 2.170 ... (remaining 79807 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: 1.360 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.006 0.092 9518 Z= 0.393 Angle : 0.861 15.278 12913 Z= 0.554 Chirality : 0.053 0.377 1490 Planarity : 0.005 0.047 1606 Dihedral : 15.323 117.445 3777 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.95 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1172 helix: 1.29 (0.18), residues: 791 sheet: 0.48 (0.63), residues: 70 loop : -0.05 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.008 0.001 HIS A 932 PHE 0.041 0.002 PHE A 974 TYR 0.023 0.002 TYR A 958 ARG 0.007 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.033 Fit side-chains REVERT: A 312 TYR cc_start: 0.7271 (t80) cc_final: 0.7055 (t80) REVERT: A 404 GLN cc_start: 0.8021 (mt0) cc_final: 0.7625 (mm-40) REVERT: A 612 MET cc_start: 0.5970 (mmt) cc_final: 0.5493 (mpp) REVERT: A 1057 LYS cc_start: 0.7814 (mttt) cc_final: 0.7292 (mptt) REVERT: A 1152 GLN cc_start: 0.7339 (mt0) cc_final: 0.7048 (mp-120) REVERT: A 1208 LYS cc_start: 0.7472 (tttm) cc_final: 0.7196 (ttpt) REVERT: A 1216 LYS cc_start: 0.7381 (ttmm) cc_final: 0.6986 (mttp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 1.5498 time to fit residues: 239.6367 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.0570 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 392 ASN A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134513 restraints weight = 8668.675| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.69 r_work: 0.3343 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9518 Z= 0.158 Angle : 0.549 9.520 12913 Z= 0.286 Chirality : 0.040 0.157 1490 Planarity : 0.003 0.033 1606 Dihedral : 11.247 89.469 1685 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.89 % Allowed : 8.71 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.24), residues: 1172 helix: 1.77 (0.18), residues: 791 sheet: 0.47 (0.64), residues: 70 loop : -0.23 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.004 0.001 HIS A 932 PHE 0.028 0.002 PHE A 332 TYR 0.015 0.001 TYR A 506 ARG 0.003 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.043 Fit side-chains REVERT: A 312 TYR cc_start: 0.6968 (t80) cc_final: 0.6524 (t80) REVERT: A 402 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: A 592 ASP cc_start: 0.7223 (m-30) cc_final: 0.6899 (m-30) REVERT: A 728 PHE cc_start: 0.6942 (t80) cc_final: 0.6544 (t80) REVERT: A 872 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5189 (mtm) REVERT: A 918 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 1055 GLU cc_start: 0.7757 (tp30) cc_final: 0.7536 (tp30) REVERT: A 1057 LYS cc_start: 0.6743 (mttt) cc_final: 0.5683 (mptt) REVERT: A 1096 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: A 1152 GLN cc_start: 0.7858 (mt0) cc_final: 0.6654 (mp-120) REVERT: A 1159 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: A 1208 LYS cc_start: 0.6745 (tttm) cc_final: 0.6074 (ttpt) REVERT: A 1215 ASP cc_start: 0.7133 (m-30) cc_final: 0.6822 (m-30) REVERT: A 1216 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6391 (mttp) REVERT: A 1246 LYS cc_start: 0.6796 (mttp) cc_final: 0.5937 (mmtm) outliers start: 18 outliers final: 2 residues processed: 128 average time/residue: 1.5533 time to fit residues: 210.2702 Evaluate side-chains 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1164 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131680 restraints weight = 8664.972| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.68 r_work: 0.3326 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.191 Angle : 0.537 9.107 12913 Z= 0.279 Chirality : 0.040 0.151 1490 Planarity : 0.003 0.031 1606 Dihedral : 10.711 88.697 1685 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 1.89 % Allowed : 11.86 % Favored : 86.25 % 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: 1.71 (0.24), residues: 1172 helix: 1.69 (0.18), residues: 802 sheet: 0.54 (0.63), residues: 70 loop : -0.10 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.004 0.001 HIS A1151 PHE 0.020 0.002 PHE A 508 TYR 0.011 0.001 TYR A 849 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.925 Fit side-chains REVERT: A 312 TYR cc_start: 0.6987 (t80) cc_final: 0.6538 (t80) REVERT: A 402 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: A 404 GLN cc_start: 0.8355 (mt0) cc_final: 0.7288 (mm-40) REVERT: A 592 ASP cc_start: 0.7321 (m-30) cc_final: 0.7041 (m-30) REVERT: A 612 MET cc_start: 0.5516 (mmt) cc_final: 0.4873 (mmm) REVERT: A 753 LEU cc_start: 0.7261 (tt) cc_final: 0.6758 (tm) REVERT: A 872 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5214 (mtm) REVERT: A 918 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 1057 LYS cc_start: 0.6778 (mttt) cc_final: 0.5714 (mptt) REVERT: A 1096 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: A 1152 GLN cc_start: 0.7918 (mt0) cc_final: 0.6721 (mp-120) REVERT: A 1208 LYS cc_start: 0.6814 (tttm) cc_final: 0.6117 (ttpt) REVERT: A 1215 ASP cc_start: 0.7114 (m-30) cc_final: 0.6855 (m-30) REVERT: A 1246 LYS cc_start: 0.6975 (mttp) cc_final: 0.6770 (mttp) outliers start: 18 outliers final: 3 residues processed: 137 average time/residue: 1.4877 time to fit residues: 216.3626 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1203 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.182570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130651 restraints weight = 8624.311| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.68 r_work: 0.3300 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9518 Z= 0.173 Angle : 0.507 7.457 12913 Z= 0.265 Chirality : 0.040 0.162 1490 Planarity : 0.003 0.031 1606 Dihedral : 10.166 87.822 1685 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.21 % Rotamer: Outliers : 3.25 % Allowed : 11.86 % Favored : 84.89 % 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: 1.77 (0.24), residues: 1172 helix: 1.76 (0.18), residues: 800 sheet: 0.56 (0.63), residues: 70 loop : -0.17 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.004 0.001 HIS A1003 PHE 0.019 0.001 PHE A 508 TYR 0.010 0.001 TYR A 849 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.860 Fit side-chains REVERT: A 204 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: A 221 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6280 (mp) REVERT: A 312 TYR cc_start: 0.7069 (t80) cc_final: 0.6615 (t80) REVERT: A 402 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: A 404 GLN cc_start: 0.8357 (mt0) cc_final: 0.7263 (mm-40) REVERT: A 444 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7834 (t70) REVERT: A 592 ASP cc_start: 0.7289 (m-30) cc_final: 0.6989 (m-30) REVERT: A 612 MET cc_start: 0.5579 (mmt) cc_final: 0.4871 (mmm) REVERT: A 753 LEU cc_start: 0.7294 (tt) cc_final: 0.6788 (tm) REVERT: A 872 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5299 (mtm) REVERT: A 918 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 928 MET cc_start: 0.8733 (mmp) cc_final: 0.8487 (mmp) REVERT: A 953 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 954 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6605 (tpt-90) REVERT: A 1057 LYS cc_start: 0.6779 (mttt) cc_final: 0.5693 (mptt) REVERT: A 1096 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: A 1152 GLN cc_start: 0.7921 (mt0) cc_final: 0.6700 (mp-120) REVERT: A 1208 LYS cc_start: 0.6794 (tttm) cc_final: 0.6089 (ttpt) REVERT: A 1215 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: A 1246 LYS cc_start: 0.7045 (mttp) cc_final: 0.6825 (mttp) outliers start: 31 outliers final: 6 residues processed: 137 average time/residue: 1.5513 time to fit residues: 224.9534 Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 HIS A1030 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.184351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132773 restraints weight = 8663.480| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.68 r_work: 0.3342 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9518 Z= 0.132 Angle : 0.468 7.364 12913 Z= 0.248 Chirality : 0.038 0.173 1490 Planarity : 0.003 0.029 1606 Dihedral : 9.828 86.854 1685 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 2.94 % Allowed : 12.91 % Favored : 84.16 % 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: 1.98 (0.24), residues: 1172 helix: 1.96 (0.18), residues: 797 sheet: 0.57 (0.62), residues: 70 loop : -0.19 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS A1003 PHE 0.018 0.001 PHE A 763 TYR 0.008 0.001 TYR A 440 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.958 Fit side-chains REVERT: A 204 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: A 221 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6245 (mp) REVERT: A 312 TYR cc_start: 0.7011 (t80) cc_final: 0.6584 (t80) REVERT: A 392 ASN cc_start: 0.7941 (t0) cc_final: 0.7696 (t0) REVERT: A 402 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: A 566 GLN cc_start: 0.6955 (tp40) cc_final: 0.6656 (mm110) REVERT: A 592 ASP cc_start: 0.7282 (m-30) cc_final: 0.6969 (m-30) REVERT: A 612 MET cc_start: 0.5557 (mmt) cc_final: 0.4841 (mmm) REVERT: A 725 SER cc_start: 0.7927 (t) cc_final: 0.7683 (p) REVERT: A 753 LEU cc_start: 0.7250 (tt) cc_final: 0.6738 (tm) REVERT: A 872 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5463 (mtm) REVERT: A 928 MET cc_start: 0.8668 (mmp) cc_final: 0.8450 (mmp) REVERT: A 953 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 954 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6610 (tpt-90) REVERT: A 961 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6473 (p) REVERT: A 968 GLU cc_start: 0.7351 (mp0) cc_final: 0.6489 (mt-10) REVERT: A 1030 ASN cc_start: 0.8253 (m-40) cc_final: 0.7719 (m-40) REVERT: A 1057 LYS cc_start: 0.6813 (mttt) cc_final: 0.5750 (mptt) REVERT: A 1152 GLN cc_start: 0.7912 (mt0) cc_final: 0.6708 (mp-120) REVERT: A 1208 LYS cc_start: 0.6832 (tttm) cc_final: 0.6111 (ttpt) REVERT: A 1215 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: A 1246 LYS cc_start: 0.7008 (mttp) cc_final: 0.6791 (mttp) outliers start: 28 outliers final: 5 residues processed: 138 average time/residue: 1.3427 time to fit residues: 198.0640 Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN A1099 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131374 restraints weight = 8611.622| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.67 r_work: 0.3328 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9518 Z= 0.151 Angle : 0.474 7.252 12913 Z= 0.252 Chirality : 0.039 0.189 1490 Planarity : 0.003 0.029 1606 Dihedral : 9.814 86.208 1685 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 1.89 % Allowed : 14.59 % Favored : 83.53 % 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: 1.95 (0.24), residues: 1172 helix: 1.94 (0.18), residues: 797 sheet: 0.57 (0.62), residues: 70 loop : -0.18 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.018 0.001 PHE A 508 TYR 0.014 0.001 TYR A 506 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.927 Fit side-chains REVERT: A 201 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7155 (mt) REVERT: A 204 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 221 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 312 TYR cc_start: 0.7036 (t80) cc_final: 0.6602 (t80) REVERT: A 392 ASN cc_start: 0.8017 (t0) cc_final: 0.7752 (t0) REVERT: A 402 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: A 510 MET cc_start: 0.8293 (mpp) cc_final: 0.7831 (mpp) REVERT: A 566 GLN cc_start: 0.6938 (tp40) cc_final: 0.6696 (mm110) REVERT: A 592 ASP cc_start: 0.7185 (m-30) cc_final: 0.6866 (m-30) REVERT: A 612 MET cc_start: 0.5651 (mmt) cc_final: 0.4950 (mmm) REVERT: A 725 SER cc_start: 0.7953 (t) cc_final: 0.7710 (p) REVERT: A 753 LEU cc_start: 0.7248 (tt) cc_final: 0.6728 (tm) REVERT: A 872 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5476 (mtm) REVERT: A 918 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 946 TYR cc_start: 0.8198 (m-80) cc_final: 0.7990 (m-80) REVERT: A 953 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 954 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6637 (tpt-90) REVERT: A 961 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6486 (p) REVERT: A 968 GLU cc_start: 0.7302 (mp0) cc_final: 0.6454 (mt-10) REVERT: A 1030 ASN cc_start: 0.8256 (m-40) cc_final: 0.7765 (m-40) REVERT: A 1057 LYS cc_start: 0.6833 (mttt) cc_final: 0.5761 (mptt) REVERT: A 1152 GLN cc_start: 0.7916 (mt0) cc_final: 0.6706 (mp-120) REVERT: A 1215 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: A 1246 LYS cc_start: 0.7014 (mttp) cc_final: 0.6144 (mmtm) outliers start: 18 outliers final: 5 residues processed: 134 average time/residue: 1.4186 time to fit residues: 202.2798 Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 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 = 0.4003 r_free = 0.4003 target = 0.180356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128067 restraints weight = 8707.866| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.69 r_work: 0.3282 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9518 Z= 0.215 Angle : 0.511 7.135 12913 Z= 0.270 Chirality : 0.040 0.198 1490 Planarity : 0.003 0.029 1606 Dihedral : 10.019 84.689 1685 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.10 % Allowed : 15.74 % Favored : 82.16 % 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: 1.79 (0.24), residues: 1172 helix: 1.77 (0.18), residues: 799 sheet: 0.56 (0.63), residues: 70 loop : -0.14 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.003 0.001 HIS A1151 PHE 0.023 0.002 PHE A 508 TYR 0.013 0.001 TYR A 849 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.000 Fit side-chains REVERT: A 112 TYR cc_start: 0.6950 (m-80) cc_final: 0.6721 (m-80) REVERT: A 204 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 221 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6277 (mp) REVERT: A 312 TYR cc_start: 0.7048 (t80) cc_final: 0.6627 (t80) REVERT: A 392 ASN cc_start: 0.8002 (t0) cc_final: 0.7728 (t0) REVERT: A 402 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: A 404 GLN cc_start: 0.8374 (mt0) cc_final: 0.7273 (mm-40) REVERT: A 510 MET cc_start: 0.8269 (tpp) cc_final: 0.7965 (mpp) REVERT: A 566 GLN cc_start: 0.6922 (tp40) cc_final: 0.6622 (mm110) REVERT: A 592 ASP cc_start: 0.7251 (m-30) cc_final: 0.6959 (m-30) REVERT: A 612 MET cc_start: 0.5710 (mmt) cc_final: 0.5014 (mmm) REVERT: A 753 LEU cc_start: 0.7286 (tt) cc_final: 0.6742 (tm) REVERT: A 804 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7725 (mttm) REVERT: A 846 SER cc_start: 0.6799 (m) cc_final: 0.6557 (p) REVERT: A 872 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5456 (mtm) REVERT: A 918 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: A 928 MET cc_start: 0.8747 (mmp) cc_final: 0.8512 (mmp) REVERT: A 954 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6706 (tpt-90) REVERT: A 961 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6524 (p) REVERT: A 968 GLU cc_start: 0.7343 (mp0) cc_final: 0.6476 (mt-10) REVERT: A 1057 LYS cc_start: 0.6840 (mttt) cc_final: 0.5751 (mptt) REVERT: A 1152 GLN cc_start: 0.7912 (mt0) cc_final: 0.6695 (mp-120) REVERT: A 1215 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: A 1243 GLN cc_start: 0.6612 (mm-40) cc_final: 0.6400 (mt0) REVERT: A 1246 LYS cc_start: 0.7165 (mttp) cc_final: 0.6276 (mmtm) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 1.4097 time to fit residues: 196.3871 Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.177270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124773 restraints weight = 8814.681| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.69 r_work: 0.3236 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9518 Z= 0.286 Angle : 0.565 8.020 12913 Z= 0.296 Chirality : 0.042 0.204 1490 Planarity : 0.004 0.033 1606 Dihedral : 10.250 83.607 1685 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % 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: 1.53 (0.24), residues: 1172 helix: 1.56 (0.18), residues: 799 sheet: 0.85 (0.71), residues: 60 loop : -0.24 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.004 0.001 HIS A1151 PHE 0.029 0.002 PHE A 508 TYR 0.014 0.002 TYR A 946 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.047 Fit side-chains REVERT: A 112 TYR cc_start: 0.7136 (m-80) cc_final: 0.6877 (m-80) REVERT: A 114 TYR cc_start: 0.7749 (m-80) cc_final: 0.7383 (m-80) REVERT: A 204 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7217 (m-80) REVERT: A 221 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6300 (mp) REVERT: A 312 TYR cc_start: 0.7066 (t80) cc_final: 0.6658 (t80) REVERT: A 392 ASN cc_start: 0.8081 (t0) cc_final: 0.7801 (t0) REVERT: A 402 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 404 GLN cc_start: 0.8376 (mt0) cc_final: 0.7278 (mm-40) REVERT: A 510 MET cc_start: 0.8260 (tpp) cc_final: 0.7770 (mpp) REVERT: A 566 GLN cc_start: 0.6897 (tp40) cc_final: 0.6618 (mm110) REVERT: A 592 ASP cc_start: 0.7238 (m-30) cc_final: 0.6960 (m-30) REVERT: A 612 MET cc_start: 0.5645 (mmt) cc_final: 0.4883 (mmm) REVERT: A 753 LEU cc_start: 0.7288 (tt) cc_final: 0.6756 (tm) REVERT: A 846 SER cc_start: 0.6809 (m) cc_final: 0.6556 (p) REVERT: A 872 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5538 (mtm) REVERT: A 918 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: A 928 MET cc_start: 0.8768 (mmp) cc_final: 0.8553 (mmp) REVERT: A 954 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6732 (tpt-90) REVERT: A 961 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6529 (p) REVERT: A 968 GLU cc_start: 0.7326 (mp0) cc_final: 0.6462 (mt-10) REVERT: A 1030 ASN cc_start: 0.8350 (m-40) cc_final: 0.7835 (m-40) REVERT: A 1057 LYS cc_start: 0.6867 (mttt) cc_final: 0.5813 (mptt) REVERT: A 1152 GLN cc_start: 0.7906 (mt0) cc_final: 0.6694 (mp-120) REVERT: A 1215 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: A 1243 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6435 (mt0) outliers start: 24 outliers final: 10 residues processed: 138 average time/residue: 1.4181 time to fit residues: 207.9034 Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.180637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128841 restraints weight = 8725.994| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.68 r_work: 0.3294 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9518 Z= 0.165 Angle : 0.505 9.002 12913 Z= 0.263 Chirality : 0.039 0.192 1490 Planarity : 0.003 0.029 1606 Dihedral : 10.076 82.382 1685 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 16.47 % Favored : 81.64 % 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: 1.68 (0.24), residues: 1172 helix: 1.73 (0.18), residues: 805 sheet: 0.45 (0.63), residues: 70 loop : -0.32 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.023 0.001 PHE A 332 TYR 0.011 0.001 TYR A 849 ARG 0.004 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.910 Fit side-chains REVERT: A 112 TYR cc_start: 0.7122 (m-80) cc_final: 0.6888 (m-80) REVERT: A 114 TYR cc_start: 0.7678 (m-80) cc_final: 0.7240 (m-80) REVERT: A 204 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: A 221 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6243 (mp) REVERT: A 312 TYR cc_start: 0.7021 (t80) cc_final: 0.6593 (t80) REVERT: A 376 LYS cc_start: 0.8516 (mttt) cc_final: 0.7912 (mmtt) REVERT: A 392 ASN cc_start: 0.7970 (t0) cc_final: 0.7649 (t0) REVERT: A 402 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: A 404 GLN cc_start: 0.8379 (mt0) cc_final: 0.7272 (mm-40) REVERT: A 510 MET cc_start: 0.8355 (tpp) cc_final: 0.7828 (mpp) REVERT: A 566 GLN cc_start: 0.6910 (tp40) cc_final: 0.6651 (mm110) REVERT: A 592 ASP cc_start: 0.7232 (m-30) cc_final: 0.6958 (m-30) REVERT: A 612 MET cc_start: 0.5644 (mmt) cc_final: 0.4954 (mmm) REVERT: A 753 LEU cc_start: 0.7322 (tt) cc_final: 0.6791 (tm) REVERT: A 846 SER cc_start: 0.6851 (m) cc_final: 0.6615 (p) REVERT: A 872 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.5628 (mtm) REVERT: A 918 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 954 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6696 (tpt-90) REVERT: A 961 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6483 (p) REVERT: A 968 GLU cc_start: 0.7305 (mp0) cc_final: 0.6442 (mt-10) REVERT: A 1030 ASN cc_start: 0.8302 (m-40) cc_final: 0.7827 (m-40) REVERT: A 1057 LYS cc_start: 0.6827 (mttt) cc_final: 0.5765 (mptt) REVERT: A 1152 GLN cc_start: 0.7872 (mt0) cc_final: 0.6674 (mp-120) REVERT: A 1215 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: A 1243 GLN cc_start: 0.6644 (mm-40) cc_final: 0.6409 (mt0) REVERT: A 1246 LYS cc_start: 0.7475 (mttp) cc_final: 0.6343 (mmtm) outliers start: 18 outliers final: 5 residues processed: 130 average time/residue: 1.6735 time to fit residues: 231.2845 Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.180028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128137 restraints weight = 8792.194| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.68 r_work: 0.3288 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9518 Z= 0.182 Angle : 0.515 9.028 12913 Z= 0.268 Chirality : 0.039 0.212 1490 Planarity : 0.003 0.030 1606 Dihedral : 9.939 83.599 1685 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 2.10 % Allowed : 16.26 % Favored : 81.64 % 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: 1.68 (0.24), residues: 1172 helix: 1.71 (0.18), residues: 807 sheet: 0.46 (0.63), residues: 70 loop : -0.29 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS A1151 PHE 0.028 0.002 PHE A 332 TYR 0.011 0.001 TYR A 506 ARG 0.004 0.000 ARG A 954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.019 Fit side-chains REVERT: A 112 TYR cc_start: 0.7127 (m-80) cc_final: 0.6903 (m-80) REVERT: A 114 TYR cc_start: 0.7650 (m-80) cc_final: 0.7197 (m-80) REVERT: A 204 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: A 221 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6242 (mp) REVERT: A 312 TYR cc_start: 0.7045 (t80) cc_final: 0.6616 (t80) REVERT: A 376 LYS cc_start: 0.8506 (mttt) cc_final: 0.7900 (mmtt) REVERT: A 392 ASN cc_start: 0.7944 (t0) cc_final: 0.7625 (t0) REVERT: A 402 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: A 404 GLN cc_start: 0.8376 (mt0) cc_final: 0.7270 (mm-40) REVERT: A 510 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7830 (mpp) REVERT: A 566 GLN cc_start: 0.6894 (tp40) cc_final: 0.6644 (mm110) REVERT: A 592 ASP cc_start: 0.7274 (m-30) cc_final: 0.6975 (m-30) REVERT: A 612 MET cc_start: 0.5658 (mmt) cc_final: 0.4972 (mmm) REVERT: A 753 LEU cc_start: 0.7348 (tt) cc_final: 0.6789 (tm) REVERT: A 804 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7763 (mtmm) REVERT: A 846 SER cc_start: 0.6859 (m) cc_final: 0.6623 (p) REVERT: A 872 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.5682 (mtm) REVERT: A 918 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 954 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6717 (tpt-90) REVERT: A 961 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6512 (p) REVERT: A 968 GLU cc_start: 0.7264 (mp0) cc_final: 0.6447 (mt-10) REVERT: A 1030 ASN cc_start: 0.8275 (m-40) cc_final: 0.7826 (m-40) REVERT: A 1057 LYS cc_start: 0.6787 (mttt) cc_final: 0.5743 (mptt) REVERT: A 1152 GLN cc_start: 0.7894 (mt0) cc_final: 0.6675 (mp-120) REVERT: A 1215 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: A 1243 GLN cc_start: 0.6667 (mm-40) cc_final: 0.6415 (mt0) REVERT: A 1246 LYS cc_start: 0.7483 (mttp) cc_final: 0.6371 (mmtm) outliers start: 20 outliers final: 6 residues processed: 128 average time/residue: 1.4710 time to fit residues: 200.2972 Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 918 GLN Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.180994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129173 restraints weight = 8754.850| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.68 r_work: 0.3296 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9518 Z= 0.170 Angle : 0.504 8.738 12913 Z= 0.263 Chirality : 0.039 0.206 1490 Planarity : 0.003 0.030 1606 Dihedral : 9.802 82.446 1685 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.87 % Rotamer: Outliers : 1.99 % Allowed : 16.37 % Favored : 81.64 % 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: 1.73 (0.24), residues: 1172 helix: 1.75 (0.18), residues: 807 sheet: 0.46 (0.63), residues: 70 loop : -0.28 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.031 0.001 PHE A 332 TYR 0.011 0.001 TYR A 306 ARG 0.004 0.000 ARG A 954 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8277.75 seconds wall clock time: 144 minutes 2.71 seconds (8642.71 seconds total)