Starting phenix.real_space_refine on Tue Feb 3 17:17:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pec_71557/02_2026/9pec_71557.map" } resolution = 3.29 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= 0.023 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 27 5.16 5 C 3422 2.51 5 N 924 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 5383 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5356 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 643} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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 860 SG CYS A 800 30.501 27.004 68.540 1.00 84.90 S ATOM 1511 SG CYS A 880 26.875 27.563 68.644 1.00 95.00 S ATOM 1530 SG CYS A 883 30.065 24.660 66.930 1.00116.14 S Time building chain proxies: 1.16, per 1000 atoms: 0.22 Number of scatterers: 5383 At special positions: 0 Unit cell: (57.54, 95.9, 106.449, 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 27 16.00 O 1009 8.00 N 924 7.00 C 3422 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: 0.26 Conformation dependent library (CDL) restraints added in 263.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 880 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 800 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 773 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 883 " Number of angles added : 3 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 32.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 630 through 642 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 removed outlier: 3.843A pdb=" N ALA A 788 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 846 removed outlier: 3.930A pdb=" N ALA A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 841 " --> pdb=" O TRP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.934A pdb=" N VAL A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 981 " --> pdb=" O PRO A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 981 through 987 removed outlier: 3.514A pdb=" N ALA A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) 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 1112 Processing helix chain 'A' and resid 1124 through 1135 Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1176 through 1182 Processing helix chain 'A' and resid 1221 through 1231 Processing helix chain 'A' and resid 1242 through 1248 removed outlier: 3.856A pdb=" N PHE A1246 " --> pdb=" O PHE A1243 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN A1247 " --> pdb=" O VAL A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1263 Processing helix chain 'A' and resid 1274 through 1276 No H-bonds generated for 'chain 'A' and resid 1274 through 1276' Processing helix chain 'A' and resid 1338 through 1343 Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.928A pdb=" N GLY A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1485 Processing helix chain 'A' and resid 1496 through 1506 Processing helix chain 'A' and resid 1509 through 1526 Processing sheet with id=AA1, first strand: chain 'A' and resid 710 through 713 removed outlier: 4.495A pdb=" N GLN A 729 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 719 removed outlier: 4.183A pdb=" N GLY A 718 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 794 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR A 858 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU A 796 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 815 " --> pdb=" O CYS A 854 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER A 856 " --> pdb=" O GLU A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.598A pdb=" N THR A 744 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 811 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A 742 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 794 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR A 858 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU A 796 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 903 through 906 Processing sheet with id=AA5, first strand: chain 'A' and resid 994 through 1002 removed outlier: 7.343A pdb=" N SER A 996 " --> pdb=" O TYR A 975 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR A 975 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP A 998 " --> pdb=" O ARG A 973 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 972 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 951 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 974 " --> pdb=" O CYS A 949 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS A 949 " --> pdb=" O PHE A 974 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 916 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A1009 " --> pdb=" O TYR A 918 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1013 through 1014 Processing sheet with id=AA7, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.515A pdb=" N THR A1139 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A1093 " --> pdb=" O SER A1115 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA A1117 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A1095 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP A1119 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A1094 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN A1193 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A1096 " --> pdb=" O ASN A1193 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A1192 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLU A1238 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A1194 " --> pdb=" O GLU A1238 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N VAL A1240 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1312 through 1314 Processing sheet with id=AA9, first strand: chain 'A' and resid 1357 through 1358 200 hydrogen bonds defined for protein. 564 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: 0.84 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1768 1.35 - 1.46: 1286 1.46 - 1.58: 2411 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5504 Sorted by residual: bond pdb=" N VAL A1142 " pdb=" CA VAL A1142 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.06e+00 bond pdb=" CA ASP A 767 " pdb=" CB ASP A 767 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.74e-02 3.30e+03 8.38e-01 bond pdb=" CB ASP A 767 " pdb=" CG ASP A 767 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.58e-01 bond pdb=" C PRO A1510 " pdb=" N PRO A1511 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.66e-01 bond pdb=" CB MET A 771 " pdb=" CG MET A 771 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.02e-01 ... (remaining 5499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 7375 2.36 - 4.71: 51 4.71 - 7.07: 7 7.07 - 9.43: 3 9.43 - 11.79: 1 Bond angle restraints: 7437 Sorted by residual: angle pdb=" CA LEU A1221 " pdb=" CB LEU A1221 " pdb=" CG LEU A1221 " ideal model delta sigma weight residual 116.30 128.09 -11.79 3.50e+00 8.16e-02 1.13e+01 angle pdb=" C ILE A1220 " pdb=" N LEU A1221 " pdb=" CA LEU A1221 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N VAL A1142 " pdb=" CA VAL A1142 " pdb=" C VAL A1142 " ideal model delta sigma weight residual 106.21 109.17 -2.96 1.07e+00 8.73e-01 7.64e+00 angle pdb=" CA LEU A 805 " pdb=" CB LEU A 805 " pdb=" CG LEU A 805 " ideal model delta sigma weight residual 116.30 125.52 -9.22 3.50e+00 8.16e-02 6.94e+00 angle pdb=" CB MET A 771 " pdb=" CG MET A 771 " pdb=" SD MET A 771 " ideal model delta sigma weight residual 112.70 120.07 -7.37 3.00e+00 1.11e-01 6.03e+00 ... (remaining 7432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 2759 17.66 - 35.31: 386 35.31 - 52.97: 115 52.97 - 70.62: 22 70.62 - 88.28: 7 Dihedral angle restraints: 3289 sinusoidal: 1337 harmonic: 1952 Sorted by residual: dihedral pdb=" CA TYR A1264 " pdb=" C TYR A1264 " pdb=" N GLN A1265 " pdb=" CA GLN A1265 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU A1471 " pdb=" CG GLU A1471 " pdb=" CD GLU A1471 " pdb=" OE1 GLU A1471 " ideal model delta sinusoidal sigma weight residual 0.00 88.28 -88.28 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB MET A1262 " pdb=" CG MET A1262 " pdb=" SD MET A1262 " pdb=" CE MET A1262 " ideal model delta sinusoidal sigma weight residual -180.00 -121.10 -58.90 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 466 0.024 - 0.048: 195 0.048 - 0.072: 74 0.072 - 0.096: 34 0.096 - 0.121: 34 Chirality restraints: 803 Sorted by residual: chirality pdb=" CA ILE A1336 " pdb=" N ILE A1336 " pdb=" C ILE A1336 " pdb=" CB ILE A1336 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE A1313 " pdb=" N ILE A1313 " pdb=" C ILE A1313 " pdb=" CB ILE A1313 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE A 954 " pdb=" N ILE A 954 " pdb=" C ILE A 954 " pdb=" CB ILE A 954 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 800 not shown) Planarity restraints: 964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1221 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C LEU A1221 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A1221 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A1222 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1509 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A1510 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1510 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1510 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1331 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A1332 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1332 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1332 " -0.020 5.00e-02 4.00e+02 ... (remaining 961 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 740 2.76 - 3.29: 4896 3.29 - 3.83: 8470 3.83 - 4.36: 9394 4.36 - 4.90: 17173 Nonbonded interactions: 40673 Sorted by model distance: nonbonded pdb=" O LYS A 828 " pdb=" OG1 THR A 831 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A1375 " pdb=" OD2 ASP A1489 " model vdw 2.225 3.040 nonbonded pdb=" O LYS A 984 " pdb=" OG SER A 988 " model vdw 2.249 3.040 nonbonded pdb=" N GLU A 983 " pdb=" OE1 GLU A 983 " model vdw 2.322 3.120 nonbonded pdb=" NE2 GLN A1265 " pdb=" O ALA A1291 " model vdw 2.330 3.120 ... (remaining 40668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.007 0.416 5508 Z= 0.192 Angle : 0.799 41.340 7440 Z= 0.300 Chirality : 0.039 0.121 803 Planarity : 0.004 0.040 964 Dihedral : 18.024 88.281 2031 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.69 % Allowed : 35.42 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.12 (0.33), residues: 664 helix: 1.63 (0.38), residues: 182 sheet: -1.56 (0.51), residues: 82 loop : -0.54 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 817 TYR 0.007 0.001 TYR A1321 PHE 0.010 0.001 PHE A 758 TRP 0.011 0.001 TRP A1288 HIS 0.002 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 5504) covalent geometry : angle 0.52625 ( 7437) hydrogen bonds : bond 0.17689 ( 191) hydrogen bonds : angle 6.94704 ( 564) metal coordination : bond 0.24870 ( 4) metal coordination : angle 29.95038 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 1036 LEU cc_start: 0.6070 (pt) cc_final: 0.5805 (mt) REVERT: A 1047 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8041 (mm-40) REVERT: A 1219 MET cc_start: 0.6768 (mmt) cc_final: 0.6525 (tpp) REVERT: A 1306 PHE cc_start: 0.8552 (t80) cc_final: 0.8351 (t80) REVERT: A 1344 ASP cc_start: 0.7683 (t0) cc_final: 0.7394 (t0) REVERT: A 1352 ASP cc_start: 0.7222 (t0) cc_final: 0.6958 (t0) REVERT: A 1354 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7281 (tpp80) outliers start: 4 outliers final: 4 residues processed: 74 average time/residue: 0.0646 time to fit residues: 6.3656 Evaluate side-chains 62 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1361 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.157079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.120149 restraints weight = 7253.225| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.33 r_work: 0.3537 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5508 Z= 0.102 Angle : 0.531 9.266 7440 Z= 0.260 Chirality : 0.039 0.128 803 Planarity : 0.004 0.039 964 Dihedral : 4.814 57.315 740 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.08 % Allowed : 30.03 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.11 (0.33), residues: 664 helix: 2.06 (0.38), residues: 186 sheet: -1.30 (0.52), residues: 83 loop : -0.59 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1150 TYR 0.014 0.001 TYR A 986 PHE 0.008 0.001 PHE A1235 TRP 0.008 0.001 TRP A1288 HIS 0.002 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5504) covalent geometry : angle 0.51711 ( 7437) hydrogen bonds : bond 0.03804 ( 191) hydrogen bonds : angle 4.95641 ( 564) metal coordination : bond 0.01714 ( 4) metal coordination : angle 6.12056 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 807 ASP cc_start: 0.7049 (m-30) cc_final: 0.6733 (t0) REVERT: A 1037 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6023 (m-80) REVERT: A 1047 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8284 (mm-40) REVERT: A 1219 MET cc_start: 0.6831 (mmt) cc_final: 0.6583 (tpp) REVERT: A 1306 PHE cc_start: 0.8527 (t80) cc_final: 0.8308 (t80) REVERT: A 1344 ASP cc_start: 0.7763 (t0) cc_final: 0.7494 (t0) REVERT: A 1352 ASP cc_start: 0.7171 (t0) cc_final: 0.6740 (t0) REVERT: A 1354 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7331 (tpp80) REVERT: A 1525 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6581 (m-70) outliers start: 35 outliers final: 18 residues processed: 92 average time/residue: 0.0606 time to fit residues: 7.5462 Evaluate side-chains 78 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU 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 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1361 GLU Chi-restraints excluded: chain A residue 1525 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1381 HIS A1485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114241 restraints weight = 7524.489| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.19 r_work: 0.3450 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5508 Z= 0.203 Angle : 0.625 10.715 7440 Z= 0.315 Chirality : 0.042 0.130 803 Planarity : 0.005 0.044 964 Dihedral : 5.342 58.246 740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.42 % Allowed : 30.38 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.42 (0.32), residues: 664 helix: 1.35 (0.36), residues: 191 sheet: -1.46 (0.53), residues: 76 loop : -0.86 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1334 TYR 0.011 0.002 TYR A 852 PHE 0.017 0.002 PHE A 758 TRP 0.011 0.001 TRP A1288 HIS 0.004 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 5504) covalent geometry : angle 0.61192 ( 7437) hydrogen bonds : bond 0.04800 ( 191) hydrogen bonds : angle 5.16152 ( 564) metal coordination : bond 0.01562 ( 4) metal coordination : angle 6.29602 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 1037 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: A 1047 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8336 (mm-40) REVERT: A 1216 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6215 (pt0) REVERT: A 1306 PHE cc_start: 0.8391 (t80) cc_final: 0.8146 (t80) REVERT: A 1339 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.5876 (mtp-110) REVERT: A 1352 ASP cc_start: 0.7149 (t0) cc_final: 0.6787 (t0) REVERT: A 1354 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7574 (tpp80) REVERT: A 1380 ASP cc_start: 0.8073 (m-30) cc_final: 0.7586 (m-30) outliers start: 37 outliers final: 28 residues processed: 90 average time/residue: 0.0621 time to fit residues: 7.4545 Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 888 ASP 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 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1361 GLU Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1469 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117604 restraints weight = 7395.009| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.22 r_work: 0.3495 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5508 Z= 0.103 Angle : 0.515 10.433 7440 Z= 0.256 Chirality : 0.039 0.124 803 Planarity : 0.004 0.040 964 Dihedral : 4.955 58.456 740 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.86 % Allowed : 30.73 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.13 (0.33), residues: 664 helix: 1.76 (0.37), residues: 191 sheet: -1.30 (0.47), residues: 91 loop : -0.73 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1334 TYR 0.012 0.001 TYR A1321 PHE 0.009 0.001 PHE A1235 TRP 0.007 0.001 TRP A1299 HIS 0.002 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5504) covalent geometry : angle 0.50960 ( 7437) hydrogen bonds : bond 0.03491 ( 191) hydrogen bonds : angle 4.80678 ( 564) metal coordination : bond 0.01277 ( 4) metal coordination : angle 3.87234 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.127 Fit side-chains REVERT: A 807 ASP cc_start: 0.6898 (m-30) cc_final: 0.6667 (t0) REVERT: A 1037 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: A 1047 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8333 (mm-40) REVERT: A 1216 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5491 (pt0) REVERT: A 1306 PHE cc_start: 0.8450 (t80) cc_final: 0.8233 (t80) REVERT: A 1320 HIS cc_start: 0.7162 (p90) cc_final: 0.6947 (p90) REVERT: A 1339 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5908 (mtp-110) REVERT: A 1352 ASP cc_start: 0.7166 (t0) cc_final: 0.6768 (t0) REVERT: A 1354 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7462 (tpp80) REVERT: A 1380 ASP cc_start: 0.8067 (m-30) cc_final: 0.7596 (m-30) REVERT: A 1525 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6442 (m-70) outliers start: 28 outliers final: 19 residues processed: 85 average time/residue: 0.0548 time to fit residues: 6.4087 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU 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 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1525 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 0.0170 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.155003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119634 restraints weight = 7527.005| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.25 r_work: 0.3523 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5508 Z= 0.088 Angle : 0.502 10.550 7440 Z= 0.248 Chirality : 0.039 0.126 803 Planarity : 0.004 0.039 964 Dihedral : 4.008 35.968 737 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.99 % Allowed : 30.90 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 664 helix: 1.94 (0.38), residues: 191 sheet: -1.36 (0.47), residues: 92 loop : -0.65 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.011 0.001 TYR A1321 PHE 0.009 0.001 PHE A1235 TRP 0.007 0.001 TRP A1299 HIS 0.001 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 5504) covalent geometry : angle 0.49810 ( 7437) hydrogen bonds : bond 0.03099 ( 191) hydrogen bonds : angle 4.60015 ( 564) metal coordination : bond 0.01115 ( 4) metal coordination : angle 3.08763 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.131 Fit side-chains REVERT: A 807 ASP cc_start: 0.6953 (m-30) cc_final: 0.6707 (t0) REVERT: A 1037 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: A 1047 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8264 (mm-40) REVERT: A 1216 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5566 (pt0) REVERT: A 1306 PHE cc_start: 0.8494 (t80) cc_final: 0.8269 (t80) REVERT: A 1320 HIS cc_start: 0.7167 (p90) cc_final: 0.6915 (p90) REVERT: A 1339 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5921 (mtp-110) REVERT: A 1352 ASP cc_start: 0.6975 (t0) cc_final: 0.6696 (t0) REVERT: A 1354 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7487 (tpp80) REVERT: A 1380 ASP cc_start: 0.8011 (m-30) cc_final: 0.7549 (m-30) REVERT: A 1525 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6484 (m-70) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.0608 time to fit residues: 6.5915 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1525 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.154519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.119715 restraints weight = 7478.885| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.18 r_work: 0.3532 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5508 Z= 0.091 Angle : 0.496 10.600 7440 Z= 0.244 Chirality : 0.039 0.124 803 Planarity : 0.004 0.040 964 Dihedral : 3.881 31.281 737 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.51 % Allowed : 30.73 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 664 helix: 2.01 (0.38), residues: 191 sheet: -1.33 (0.47), residues: 92 loop : -0.59 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.010 0.001 TYR A1321 PHE 0.008 0.001 PHE A1235 TRP 0.006 0.001 TRP A1288 HIS 0.002 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5504) covalent geometry : angle 0.49232 ( 7437) hydrogen bonds : bond 0.03041 ( 191) hydrogen bonds : angle 4.51019 ( 564) metal coordination : bond 0.00960 ( 4) metal coordination : angle 2.89599 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.174 Fit side-chains REVERT: A 807 ASP cc_start: 0.6904 (m-30) cc_final: 0.6601 (t0) REVERT: A 1037 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: A 1047 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8311 (mm-40) REVERT: A 1262 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7631 (mtt) REVERT: A 1306 PHE cc_start: 0.8442 (t80) cc_final: 0.8230 (t80) REVERT: A 1320 HIS cc_start: 0.7203 (p90) cc_final: 0.6979 (p90) REVERT: A 1339 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6003 (mtp-110) REVERT: A 1352 ASP cc_start: 0.6920 (t0) cc_final: 0.6668 (t0) REVERT: A 1354 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7500 (tpp80) REVERT: A 1469 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5893 (t-170) outliers start: 26 outliers final: 18 residues processed: 79 average time/residue: 0.0649 time to fit residues: 7.0100 Evaluate side-chains 81 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1469 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.151079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115861 restraints weight = 7548.178| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.18 r_work: 0.3461 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5508 Z= 0.147 Angle : 0.552 11.122 7440 Z= 0.275 Chirality : 0.040 0.128 803 Planarity : 0.004 0.043 964 Dihedral : 4.220 32.776 737 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.69 % Allowed : 30.38 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.05 (0.33), residues: 664 helix: 2.01 (0.37), residues: 185 sheet: -1.41 (0.47), residues: 92 loop : -0.69 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1334 TYR 0.012 0.001 TYR A1321 PHE 0.014 0.002 PHE A1099 TRP 0.008 0.001 TRP A1288 HIS 0.003 0.001 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5504) covalent geometry : angle 0.54562 ( 7437) hydrogen bonds : bond 0.03709 ( 191) hydrogen bonds : angle 4.73513 ( 564) metal coordination : bond 0.01194 ( 4) metal coordination : angle 4.04689 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.127 Fit side-chains REVERT: A 807 ASP cc_start: 0.6931 (m-30) cc_final: 0.6532 (t0) REVERT: A 1037 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: A 1047 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8310 (mm-40) REVERT: A 1306 PHE cc_start: 0.8448 (t80) cc_final: 0.8193 (t80) REVERT: A 1320 HIS cc_start: 0.7205 (p90) cc_final: 0.6930 (p90) REVERT: A 1339 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5954 (mtp-110) REVERT: A 1352 ASP cc_start: 0.6956 (t0) cc_final: 0.6667 (t0) REVERT: A 1354 ARG cc_start: 0.7850 (tpp80) cc_final: 0.7576 (tpp80) REVERT: A 1469 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5953 (t70) outliers start: 27 outliers final: 22 residues processed: 81 average time/residue: 0.0465 time to fit residues: 5.1372 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1469 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 58 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.116926 restraints weight = 7453.578| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.12 r_work: 0.3478 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5508 Z= 0.125 Angle : 0.535 11.586 7440 Z= 0.265 Chirality : 0.040 0.127 803 Planarity : 0.004 0.041 964 Dihedral : 4.177 31.458 737 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.51 % Allowed : 30.56 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 664 helix: 2.02 (0.38), residues: 185 sheet: -1.41 (0.47), residues: 92 loop : -0.67 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.012 0.001 TYR A1321 PHE 0.012 0.001 PHE A1032 TRP 0.005 0.001 TRP A1288 HIS 0.002 0.001 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5504) covalent geometry : angle 0.53028 ( 7437) hydrogen bonds : bond 0.03507 ( 191) hydrogen bonds : angle 4.70965 ( 564) metal coordination : bond 0.01211 ( 4) metal coordination : angle 3.69270 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.136 Fit side-chains REVERT: A 1037 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6342 (m-80) REVERT: A 1047 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8310 (mm-40) REVERT: A 1262 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: A 1320 HIS cc_start: 0.7163 (p90) cc_final: 0.6897 (p90) REVERT: A 1339 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5911 (mtp-110) REVERT: A 1352 ASP cc_start: 0.6953 (t0) cc_final: 0.6673 (t0) REVERT: A 1354 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7559 (tpp80) REVERT: A 1469 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.6004 (t70) outliers start: 26 outliers final: 21 residues processed: 78 average time/residue: 0.0634 time to fit residues: 6.5669 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1469 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.152436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117206 restraints weight = 7467.084| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.19 r_work: 0.3456 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5508 Z= 0.107 Angle : 0.533 11.773 7440 Z= 0.262 Chirality : 0.040 0.126 803 Planarity : 0.004 0.040 964 Dihedral : 4.038 28.104 737 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.69 % Allowed : 29.69 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.05 (0.33), residues: 664 helix: 2.11 (0.38), residues: 185 sheet: -1.38 (0.47), residues: 92 loop : -0.63 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.015 0.001 TYR A1321 PHE 0.011 0.001 PHE A1493 TRP 0.006 0.001 TRP A1299 HIS 0.002 0.001 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5504) covalent geometry : angle 0.52891 ( 7437) hydrogen bonds : bond 0.03246 ( 191) hydrogen bonds : angle 4.63167 ( 564) metal coordination : bond 0.01136 ( 4) metal coordination : angle 3.23186 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.144 Fit side-chains REVERT: A 753 MET cc_start: 0.8525 (pmm) cc_final: 0.7717 (ptt) REVERT: A 1037 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: A 1047 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8321 (mm-40) REVERT: A 1262 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7657 (mtt) REVERT: A 1320 HIS cc_start: 0.7191 (p90) cc_final: 0.6923 (p90) REVERT: A 1339 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.5909 (mtp-110) REVERT: A 1354 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7533 (tpp80) REVERT: A 1469 HIS cc_start: 0.6203 (OUTLIER) cc_final: 0.5994 (t-170) REVERT: A 1525 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.6695 (m-70) outliers start: 27 outliers final: 21 residues processed: 79 average time/residue: 0.0573 time to fit residues: 6.2746 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1469 HIS Chi-restraints excluded: chain A residue 1525 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.152409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117342 restraints weight = 7476.738| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.18 r_work: 0.3461 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5508 Z= 0.111 Angle : 0.542 12.015 7440 Z= 0.267 Chirality : 0.040 0.128 803 Planarity : 0.004 0.041 964 Dihedral : 4.024 26.154 737 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.51 % Allowed : 30.03 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.33), residues: 664 helix: 2.13 (0.38), residues: 185 sheet: -1.35 (0.47), residues: 92 loop : -0.62 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.016 0.001 TYR A1321 PHE 0.009 0.001 PHE A 995 TRP 0.006 0.001 TRP A1288 HIS 0.002 0.001 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5504) covalent geometry : angle 0.53842 ( 7437) hydrogen bonds : bond 0.03251 ( 191) hydrogen bonds : angle 4.63141 ( 564) metal coordination : bond 0.01147 ( 4) metal coordination : angle 3.33759 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.209 Fit side-chains REVERT: A 753 MET cc_start: 0.8435 (pmm) cc_final: 0.7854 (ptm) REVERT: A 1037 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: A 1047 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8320 (mm-40) REVERT: A 1262 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: A 1320 HIS cc_start: 0.7199 (p90) cc_final: 0.6934 (p90) REVERT: A 1339 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5830 (mtp-110) REVERT: A 1354 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7703 (tpp80) REVERT: A 1469 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6056 (t-170) REVERT: A 1525 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.6671 (m-70) outliers start: 26 outliers final: 20 residues processed: 77 average time/residue: 0.0568 time to fit residues: 6.0638 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1339 ARG Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1469 HIS Chi-restraints excluded: chain A residue 1525 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 38 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.154602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119671 restraints weight = 7456.107| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.17 r_work: 0.3494 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5508 Z= 0.089 Angle : 0.526 11.984 7440 Z= 0.257 Chirality : 0.039 0.125 803 Planarity : 0.004 0.039 964 Dihedral : 3.777 20.254 737 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.51 % Allowed : 30.03 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.12 (0.33), residues: 664 helix: 2.09 (0.38), residues: 191 sheet: -1.32 (0.48), residues: 92 loop : -0.59 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1334 TYR 0.012 0.001 TYR A1321 PHE 0.012 0.001 PHE A1306 TRP 0.009 0.001 TRP A1299 HIS 0.001 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 5504) covalent geometry : angle 0.52321 ( 7437) hydrogen bonds : bond 0.02824 ( 191) hydrogen bonds : angle 4.48059 ( 564) metal coordination : bond 0.01010 ( 4) metal coordination : angle 2.62952 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.18 seconds wall clock time: 23 minutes 43.79 seconds (1423.79 seconds total)