Starting phenix.real_space_refine on Wed Feb 4 02:05:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9peb_71556/02_2026/9peb_71556.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.030 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 43 5.16 5 C 5184 2.51 5 N 1397 2.21 5 O 1502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8127 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8100 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 966} Chain breaks: 7 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2990 SG CYS A 800 34.920 32.288 106.439 1.00 54.26 S ATOM 3641 SG CYS A 880 37.078 34.588 109.348 1.00 80.23 S ATOM 3660 SG CYS A 883 33.355 33.590 109.537 1.00 81.81 S Time building chain proxies: 2.34, per 1000 atoms: 0.29 Number of scatterers: 8127 At special positions: 0 Unit cell: (89.904, 89.904, 138.227, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 43 16.00 O 1502 8.00 N 1397 7.00 C 5184 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: 0.80 Conformation dependent library (CDL) restraints added in 273.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1602 " pdb="ZN ZN A1602 " - pdb=" NE2 HIS A 773 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 880 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 800 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 883 " Number of angles added : 3 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 33.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.980A pdb=" N ILE A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.261A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 377' Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.521A pdb=" N LEU A 410 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.526A pdb=" N ILE A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.814A pdb=" N THR A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.991A pdb=" N ILE A 562 " --> pdb=" O HIS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 Processing helix chain 'A' and resid 577 through 587 removed outlier: 4.137A pdb=" N VAL A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 644 removed outlier: 3.655A pdb=" N ASN A 634 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 785 through 789 Processing helix chain 'A' and resid 825 through 846 removed outlier: 3.954A pdb=" N ASP A 833 " --> pdb=" O ASN A 829 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 834 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.881A pdb=" N ILE A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 981 through 987 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1103 through 1113 Processing helix chain 'A' and resid 1124 through 1135 Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.411A pdb=" N ARG A1150 " --> pdb=" O ASN A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1162 removed outlier: 3.863A pdb=" N CYS A1162 " --> pdb=" O GLN A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1174 removed outlier: 3.662A pdb=" N ASN A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A1170 " --> pdb=" O THR A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1183 removed outlier: 3.518A pdb=" N LYS A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1218 removed outlier: 3.710A pdb=" N CYS A1217 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A1218 " --> pdb=" O VAL A1215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1214 through 1218' Processing helix chain 'A' and resid 1219 through 1231 removed outlier: 3.939A pdb=" N PHE A1223 " --> pdb=" O MET A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.895A pdb=" N PHE A1246 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1263 Processing helix chain 'A' and resid 1274 through 1277 removed outlier: 3.972A pdb=" N GLY A1277 " --> pdb=" O GLY A1274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1274 through 1277' Processing helix chain 'A' and resid 1338 through 1343 Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.543A pdb=" N GLY A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1396 Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.500A pdb=" N ASP A1407 " --> pdb=" O ASP A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.530A pdb=" N LYS A1439 " --> pdb=" O ASN A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1485 removed outlier: 3.583A pdb=" N GLN A1485 " --> pdb=" O CYS A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1507 Processing helix chain 'A' and resid 1509 through 1525 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 349 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 457 removed outlier: 6.790A pdb=" N PHE A 424 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 398 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER A 426 " --> pdb=" O TRP A 396 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 396 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 391 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A 476 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 713 removed outlier: 4.395A pdb=" N GLN A 729 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 726 through 727 removed outlier: 4.243A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 726 through 727 removed outlier: 4.243A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 742 " --> pdb=" O ALA A 812 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 810 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 856 through 859 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 897 removed outlier: 3.694A pdb=" N LYS A 896 " --> pdb=" O PHE A 905 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 994 through 1002 removed outlier: 7.380A pdb=" N SER A 996 " --> pdb=" O TYR A 975 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A 975 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP A 998 " --> pdb=" O ARG A 973 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP A 968 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE A 954 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 970 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 950 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 948 " --> pdb=" O PHE A 974 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A 916 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A1010 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR A 918 " --> pdb=" O GLU A1008 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1115 through 1116 removed outlier: 3.745A pdb=" N ASP A1116 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A1095 " --> pdb=" O ASP A1116 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA A1094 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN A1193 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A1096 " --> pdb=" O ASN A1193 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A1192 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU A1238 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A1194 " --> pdb=" O GLU A1238 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N VAL A1240 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1119 through 1121 removed outlier: 6.422A pdb=" N ALA A1120 " --> pdb=" O PHE A1141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1312 through 1314 Processing sheet with id=AB3, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AB4, first strand: chain 'A' and resid 1412 through 1414 258 hydrogen bonds defined for protein. 717 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: 1.32 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2647 1.34 - 1.46: 1892 1.46 - 1.58: 3713 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 8317 Sorted by residual: bond pdb=" N ILE A 808 " pdb=" CA ILE A 808 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.22e-02 6.72e+03 8.53e+00 bond pdb=" N ASP A 807 " pdb=" CA ASP A 807 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.88e+00 bond pdb=" N ASP A1143 " pdb=" CA ASP A1143 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.32e-02 5.74e+03 7.66e+00 bond pdb=" N ASN A1144 " pdb=" CA ASN A1144 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.27e-02 6.20e+03 6.92e+00 bond pdb=" N GLN A 804 " pdb=" CA GLN A 804 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.20e+00 ... (remaining 8312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11106 1.99 - 3.99: 129 3.99 - 5.98: 13 5.98 - 7.98: 1 7.98 - 9.97: 2 Bond angle restraints: 11251 Sorted by residual: angle pdb=" CB MET A 771 " pdb=" CG MET A 771 " pdb=" SD MET A 771 " ideal model delta sigma weight residual 112.70 122.67 -9.97 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA ASP A1143 " pdb=" C ASP A1143 " pdb=" O ASP A1143 " ideal model delta sigma weight residual 121.87 118.51 3.36 1.10e+00 8.26e-01 9.33e+00 angle pdb=" CA THR A 803 " pdb=" C THR A 803 " pdb=" O THR A 803 " ideal model delta sigma weight residual 121.14 118.10 3.04 1.03e+00 9.43e-01 8.69e+00 angle pdb=" CA ASP A1143 " pdb=" CB ASP A1143 " pdb=" CG ASP A1143 " ideal model delta sigma weight residual 112.60 115.50 -2.90 1.00e+00 1.00e+00 8.40e+00 angle pdb=" CA GLU A 842 " pdb=" CB GLU A 842 " pdb=" CG GLU A 842 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.38e+00 ... (remaining 11246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4232 17.98 - 35.96: 577 35.96 - 53.93: 142 53.93 - 71.91: 26 71.91 - 89.89: 9 Dihedral angle restraints: 4986 sinusoidal: 2035 harmonic: 2951 Sorted by residual: dihedral pdb=" CA ASP A1340 " pdb=" CB ASP A1340 " pdb=" CG ASP A1340 " pdb=" OD1 ASP A1340 " ideal model delta sinusoidal sigma weight residual -30.00 -87.85 57.85 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG A 892 " pdb=" CD ARG A 892 " pdb=" NE ARG A 892 " pdb=" CZ ARG A 892 " ideal model delta sinusoidal sigma weight residual -90.00 -134.47 44.47 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 639 " pdb=" CG GLU A 639 " pdb=" CD GLU A 639 " pdb=" OE1 GLU A 639 " ideal model delta sinusoidal sigma weight residual 0.00 -87.77 87.77 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 915 0.042 - 0.084: 216 0.084 - 0.126: 85 0.126 - 0.168: 2 0.168 - 0.210: 1 Chirality restraints: 1219 Sorted by residual: chirality pdb=" CA ILE A 808 " pdb=" N ILE A 808 " pdb=" C ILE A 808 " pdb=" CB ILE A 808 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 805 " pdb=" N LEU A 805 " pdb=" C LEU A 805 " pdb=" CB LEU A 805 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA CYS A1145 " pdb=" N CYS A1145 " pdb=" C CYS A1145 " pdb=" CB CYS A1145 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1216 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A1019 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A1020 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1020 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1020 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1510 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A1511 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1511 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1511 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1509 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A1510 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1510 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1510 " 0.023 5.00e-02 4.00e+02 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1032 2.75 - 3.29: 7628 3.29 - 3.83: 12730 3.83 - 4.36: 14854 4.36 - 4.90: 25967 Nonbonded interactions: 62211 Sorted by model distance: nonbonded pdb=" O LYS A 984 " pdb=" OG SER A 988 " model vdw 2.218 3.040 nonbonded pdb=" O PHE A 776 " pdb=" OG1 THR A 797 " model vdw 2.233 3.040 nonbonded pdb=" O ILE A 406 " pdb=" OH TYR A 494 " model vdw 2.234 3.040 nonbonded pdb=" N GLN A 537 " pdb=" OE1 GLN A 537 " model vdw 2.234 3.120 nonbonded pdb=" N GLN A 626 " pdb=" OE1 GLN A 626 " model vdw 2.245 3.120 ... (remaining 62206 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: 1.680 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.367 8321 Z= 0.195 Angle : 0.553 15.689 11254 Z= 0.286 Chirality : 0.041 0.210 1219 Planarity : 0.004 0.046 1446 Dihedral : 17.354 89.889 3084 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.11 % Allowed : 31.54 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1004 helix: 0.87 (0.33), residues: 271 sheet: -0.80 (0.41), residues: 158 loop : -0.35 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 839 TYR 0.008 0.001 TYR A 377 PHE 0.013 0.001 PHE A1252 TRP 0.009 0.001 TRP A1288 HIS 0.001 0.000 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8317) covalent geometry : angle 0.51838 (11251) hydrogen bonds : bond 0.16976 ( 257) hydrogen bonds : angle 6.57980 ( 717) metal coordination : bond 0.22783 ( 4) metal coordination : angle 11.81785 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7914 (mm-40) REVERT: A 439 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5610 (pp) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.0735 time to fit residues: 12.2585 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS A 804 GLN A1501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120019 restraints weight = 11551.552| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.30 r_work: 0.3322 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8321 Z= 0.116 Angle : 0.505 6.986 11254 Z= 0.264 Chirality : 0.041 0.124 1219 Planarity : 0.004 0.050 1446 Dihedral : 3.952 27.836 1110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.74 % Allowed : 29.03 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.27), residues: 1004 helix: 1.24 (0.32), residues: 277 sheet: -0.92 (0.39), residues: 166 loop : -0.31 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 976 TYR 0.009 0.001 TYR A 554 PHE 0.018 0.002 PHE A 526 TRP 0.011 0.001 TRP A1288 HIS 0.002 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8317) covalent geometry : angle 0.50226 (11251) hydrogen bonds : bond 0.04406 ( 257) hydrogen bonds : angle 4.99708 ( 717) metal coordination : bond 0.01113 ( 4) metal coordination : angle 3.49313 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7914 (mm-40) REVERT: A 439 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5315 (pp) REVERT: A 1123 TYR cc_start: 0.6847 (t80) cc_final: 0.6289 (t80) REVERT: A 1272 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7141 (tp30) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 0.0771 time to fit residues: 14.3184 Evaluate side-chains 116 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS A1501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116897 restraints weight = 11460.790| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.49 r_work: 0.3299 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8321 Z= 0.153 Angle : 0.523 6.252 11254 Z= 0.274 Chirality : 0.042 0.134 1219 Planarity : 0.005 0.054 1446 Dihedral : 4.136 27.019 1110 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.89 % Allowed : 28.80 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.27), residues: 1004 helix: 1.44 (0.32), residues: 270 sheet: -0.94 (0.39), residues: 166 loop : -0.35 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.010 0.001 TYR A 554 PHE 0.016 0.002 PHE A1252 TRP 0.013 0.001 TRP A1288 HIS 0.010 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8317) covalent geometry : angle 0.52079 (11251) hydrogen bonds : bond 0.04600 ( 257) hydrogen bonds : angle 4.89175 ( 717) metal coordination : bond 0.00649 ( 4) metal coordination : angle 2.73878 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.5202 (pp) REVERT: A 473 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7322 (mm) REVERT: A 756 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 1123 TYR cc_start: 0.6946 (t80) cc_final: 0.6362 (t80) REVERT: A 1272 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7415 (tp30) outliers start: 34 outliers final: 18 residues processed: 130 average time/residue: 0.0756 time to fit residues: 14.5511 Evaluate side-chains 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS A1501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119707 restraints weight = 11611.133| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.32 r_work: 0.3334 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8321 Z= 0.097 Angle : 0.484 6.133 11254 Z= 0.252 Chirality : 0.040 0.126 1219 Planarity : 0.004 0.051 1446 Dihedral : 4.017 27.008 1110 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.43 % Allowed : 29.26 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 1004 helix: 1.58 (0.33), residues: 270 sheet: -0.95 (0.39), residues: 166 loop : -0.33 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1434 TYR 0.008 0.001 TYR A 377 PHE 0.016 0.001 PHE A 763 TRP 0.011 0.001 TRP A1288 HIS 0.006 0.001 HIS A1501 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8317) covalent geometry : angle 0.48354 (11251) hydrogen bonds : bond 0.03646 ( 257) hydrogen bonds : angle 4.63805 ( 717) metal coordination : bond 0.00217 ( 4) metal coordination : angle 1.63422 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 439 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5126 (pp) REVERT: A 473 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7382 (mm) REVERT: A 1123 TYR cc_start: 0.7159 (t80) cc_final: 0.6493 (t80) REVERT: A 1272 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: A 1434 ARG cc_start: 0.6783 (ptt90) cc_final: 0.6470 (pmt-80) outliers start: 30 outliers final: 16 residues processed: 134 average time/residue: 0.0697 time to fit residues: 13.9164 Evaluate side-chains 119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 6.9990 chunk 84 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118615 restraints weight = 11519.260| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.32 r_work: 0.3322 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8321 Z= 0.125 Angle : 0.503 6.438 11254 Z= 0.261 Chirality : 0.041 0.128 1219 Planarity : 0.004 0.053 1446 Dihedral : 4.080 26.836 1110 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.43 % Allowed : 28.91 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 1004 helix: 1.54 (0.33), residues: 270 sheet: -0.98 (0.39), residues: 162 loop : -0.36 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1434 TYR 0.009 0.001 TYR A 554 PHE 0.023 0.002 PHE A 514 TRP 0.012 0.001 TRP A1288 HIS 0.009 0.001 HIS A1501 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8317) covalent geometry : angle 0.50160 (11251) hydrogen bonds : bond 0.03997 ( 257) hydrogen bonds : angle 4.62887 ( 717) metal coordination : bond 0.00250 ( 4) metal coordination : angle 2.03985 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 439 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.5083 (pp) REVERT: A 454 MET cc_start: 0.7513 (ptt) cc_final: 0.7286 (ptt) REVERT: A 473 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7374 (mm) REVERT: A 1123 TYR cc_start: 0.7161 (t80) cc_final: 0.6477 (t80) REVERT: A 1272 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: A 1434 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6606 (pmt-80) outliers start: 30 outliers final: 23 residues processed: 127 average time/residue: 0.0666 time to fit residues: 13.0823 Evaluate side-chains 125 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117723 restraints weight = 11481.938| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.30 r_work: 0.3310 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8321 Z= 0.139 Angle : 0.517 6.247 11254 Z= 0.269 Chirality : 0.042 0.130 1219 Planarity : 0.004 0.054 1446 Dihedral : 4.139 26.464 1110 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.89 % Allowed : 28.80 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 1004 helix: 1.51 (0.33), residues: 270 sheet: -1.01 (0.39), residues: 162 loop : -0.40 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1434 TYR 0.010 0.001 TYR A 554 PHE 0.020 0.002 PHE A 514 TRP 0.013 0.001 TRP A1288 HIS 0.008 0.001 HIS A1501 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8317) covalent geometry : angle 0.51566 (11251) hydrogen bonds : bond 0.04166 ( 257) hydrogen bonds : angle 4.66748 ( 717) metal coordination : bond 0.00563 ( 4) metal coordination : angle 2.14749 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7387 (mm) REVERT: A 756 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 953 GLU cc_start: 0.6839 (pm20) cc_final: 0.6617 (mm-30) REVERT: A 1123 TYR cc_start: 0.7176 (t80) cc_final: 0.6469 (t80) REVERT: A 1272 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: A 1434 ARG cc_start: 0.6934 (ptt90) cc_final: 0.6576 (pmt-80) outliers start: 34 outliers final: 26 residues processed: 131 average time/residue: 0.0700 time to fit residues: 13.8383 Evaluate side-chains 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118695 restraints weight = 11491.942| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.30 r_work: 0.3326 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8321 Z= 0.111 Angle : 0.500 6.611 11254 Z= 0.259 Chirality : 0.041 0.130 1219 Planarity : 0.004 0.053 1446 Dihedral : 3.952 17.173 1108 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.89 % Allowed : 29.03 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 1004 helix: 1.59 (0.33), residues: 270 sheet: -0.96 (0.40), residues: 164 loop : -0.38 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1434 TYR 0.009 0.001 TYR A 554 PHE 0.021 0.002 PHE A 514 TRP 0.012 0.001 TRP A1288 HIS 0.002 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8317) covalent geometry : angle 0.49889 (11251) hydrogen bonds : bond 0.03770 ( 257) hydrogen bonds : angle 4.57199 ( 717) metal coordination : bond 0.00300 ( 4) metal coordination : angle 1.72376 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7364 (mm) REVERT: A 756 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 953 GLU cc_start: 0.6847 (pm20) cc_final: 0.6633 (mm-30) REVERT: A 1123 TYR cc_start: 0.7145 (t80) cc_final: 0.6589 (t80) REVERT: A 1272 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: A 1434 ARG cc_start: 0.6911 (ptt90) cc_final: 0.6560 (pmt-80) outliers start: 34 outliers final: 26 residues processed: 131 average time/residue: 0.0644 time to fit residues: 12.6398 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1501 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 99 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115967 restraints weight = 11526.683| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.27 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8321 Z= 0.171 Angle : 0.556 7.621 11254 Z= 0.288 Chirality : 0.042 0.134 1219 Planarity : 0.005 0.057 1446 Dihedral : 4.162 18.303 1108 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.00 % Allowed : 28.91 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.27), residues: 1004 helix: 1.43 (0.32), residues: 270 sheet: -1.02 (0.40), residues: 162 loop : -0.44 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.011 0.001 TYR A 554 PHE 0.021 0.002 PHE A 514 TRP 0.014 0.002 TRP A1288 HIS 0.006 0.001 HIS A1501 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8317) covalent geometry : angle 0.55479 (11251) hydrogen bonds : bond 0.04561 ( 257) hydrogen bonds : angle 4.75644 ( 717) metal coordination : bond 0.00954 ( 4) metal coordination : angle 2.37230 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7350 (mm) REVERT: A 756 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (mm) REVERT: A 1123 TYR cc_start: 0.7317 (t80) cc_final: 0.6613 (t80) REVERT: A 1272 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: A 1434 ARG cc_start: 0.6822 (ptt90) cc_final: 0.6512 (pmt-80) outliers start: 35 outliers final: 30 residues processed: 128 average time/residue: 0.0695 time to fit residues: 13.4714 Evaluate side-chains 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1459 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116991 restraints weight = 11534.039| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.28 r_work: 0.3301 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8321 Z= 0.131 Angle : 0.537 8.278 11254 Z= 0.279 Chirality : 0.042 0.133 1219 Planarity : 0.004 0.054 1446 Dihedral : 4.120 17.397 1108 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.11 % Allowed : 28.57 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.27), residues: 1004 helix: 1.49 (0.32), residues: 270 sheet: -1.07 (0.39), residues: 166 loop : -0.45 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1434 TYR 0.010 0.001 TYR A 554 PHE 0.021 0.002 PHE A 514 TRP 0.014 0.001 TRP A1288 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8317) covalent geometry : angle 0.53603 (11251) hydrogen bonds : bond 0.04079 ( 257) hydrogen bonds : angle 4.67904 ( 717) metal coordination : bond 0.00481 ( 4) metal coordination : angle 1.85100 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7359 (mm) REVERT: A 756 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 1123 TYR cc_start: 0.7230 (t80) cc_final: 0.6567 (t80) REVERT: A 1272 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: A 1434 ARG cc_start: 0.6811 (ptt90) cc_final: 0.6472 (pmt-80) outliers start: 36 outliers final: 28 residues processed: 131 average time/residue: 0.0697 time to fit residues: 13.9114 Evaluate side-chains 127 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1459 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 72 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116645 restraints weight = 11494.025| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.26 r_work: 0.3293 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8321 Z= 0.146 Angle : 0.554 8.659 11254 Z= 0.285 Chirality : 0.042 0.134 1219 Planarity : 0.005 0.055 1446 Dihedral : 4.176 17.532 1108 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.11 % Allowed : 28.69 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.27), residues: 1004 helix: 1.46 (0.32), residues: 270 sheet: -1.19 (0.39), residues: 162 loop : -0.50 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.011 0.001 TYR A 554 PHE 0.020 0.002 PHE A 514 TRP 0.013 0.001 TRP A1288 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8317) covalent geometry : angle 0.55278 (11251) hydrogen bonds : bond 0.04243 ( 257) hydrogen bonds : angle 4.74839 ( 717) metal coordination : bond 0.00536 ( 4) metal coordination : angle 2.01560 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7329 (mm) REVERT: A 736 MET cc_start: 0.7607 (tpt) cc_final: 0.7391 (tpt) REVERT: A 756 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 1123 TYR cc_start: 0.7282 (t80) cc_final: 0.6679 (t80) REVERT: A 1158 ASP cc_start: 0.6342 (p0) cc_final: 0.6130 (p0) REVERT: A 1272 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: A 1434 ARG cc_start: 0.6725 (ptt90) cc_final: 0.6486 (pmt-80) outliers start: 36 outliers final: 29 residues processed: 129 average time/residue: 0.0713 time to fit residues: 13.8746 Evaluate side-chains 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1217 CYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1459 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116650 restraints weight = 11413.353| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 8321 Z= 0.182 Angle : 0.915 59.152 11254 Z= 0.539 Chirality : 0.051 1.052 1219 Planarity : 0.005 0.055 1446 Dihedral : 4.303 35.324 1108 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 3.89 % Allowed : 29.14 % Favored : 66.97 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 1004 helix: 1.45 (0.32), residues: 270 sheet: -1.20 (0.39), residues: 162 loop : -0.49 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 976 TYR 0.011 0.001 TYR A 554 PHE 0.017 0.002 PHE A 514 TRP 0.014 0.001 TRP A1288 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8317) covalent geometry : angle 0.91456 (11251) hydrogen bonds : bond 0.04198 ( 257) hydrogen bonds : angle 4.74620 ( 717) metal coordination : bond 0.00515 ( 4) metal coordination : angle 2.00863 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.20 seconds wall clock time: 39 minutes 53.71 seconds (2393.71 seconds total)