Starting phenix.real_space_refine on Fri Aug 22 17:50:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1r_35931/08_2025/8j1r_35931.cif" } resolution = 3.52 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4187 2.51 5 N 1060 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6497 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5375 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 22, 'TRANS': 654} Chain breaks: 6 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1122 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.39, per 1000 atoms: 0.21 Number of scatterers: 6497 At special positions: 0 Unit cell: (110.622, 95.586, 81.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1225 8.00 N 1060 7.00 C 4187 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: 0.42 Conformation dependent library (CDL) restraints added in 256.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 54.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 710 through 726 removed outlier: 4.327A pdb=" N GLN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 756 through 763 removed outlier: 3.994A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.728A pdb=" N ARG A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 792 removed outlier: 4.018A pdb=" N VAL A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 810 removed outlier: 4.299A pdb=" N ILE A 801 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.516A pdb=" N LEU A 828 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 938 removed outlier: 4.025A pdb=" N VAL A 930 " --> pdb=" O THR A 926 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 938 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 994 through 1007 Processing helix chain 'A' and resid 1016 through 1029 Processing helix chain 'A' and resid 1029 through 1035 removed outlier: 4.038A pdb=" N VAL A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1050 through 1053 removed outlier: 4.104A pdb=" N PHE A1053 " --> pdb=" O PRO A1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1050 through 1053' Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 4.076A pdb=" N GLN A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1082 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1109 through 1121 Processing helix chain 'A' and resid 1139 through 1154 removed outlier: 4.166A pdb=" N THR A1143 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1217 Processing helix chain 'A' and resid 1226 through 1238 removed outlier: 3.766A pdb=" N PHE A1230 " --> pdb=" O SER A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1256 removed outlier: 3.630A pdb=" N CYS A1251 " --> pdb=" O ASP A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 Processing helix chain 'A' and resid 1275 through 1283 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1309 through 1322 Processing helix chain 'A' and resid 1323 through 1339 removed outlier: 4.763A pdb=" N LYS A1328 " --> pdb=" O LYS A1324 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLN A1329 " --> pdb=" O GLY A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.626A pdb=" N ILE A1348 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1359 removed outlier: 3.536A pdb=" N VAL A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A1356 " --> pdb=" O ASP A1352 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A1357 " --> pdb=" O GLU A1353 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A1358 " --> pdb=" O LEU A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1373 Processing helix chain 'A' and resid 1384 through 1396 removed outlier: 3.611A pdb=" N ALA A1396 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1410 removed outlier: 3.542A pdb=" N ARG A1403 " --> pdb=" O LYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1461 through 1476 removed outlier: 3.601A pdb=" N GLU A1474 " --> pdb=" O CYS A1470 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.915A pdb=" N LEU C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.719A pdb=" N ALA C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 5.858A pdb=" N GLU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 853 through 858 removed outlier: 3.529A pdb=" N ILE A 832 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS A 950 " --> pdb=" O LYS A 833 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 952 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 837 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 954 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 953 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A 914 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1100 through 1105 removed outlier: 6.578A pdb=" N ARG A1101 " --> pdb=" O GLU A1129 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU A1131 " --> pdb=" O ARG A1101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A1103 " --> pdb=" O GLU A1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1375 through 1377 removed outlier: 6.145A pdb=" N ASN A1375 " --> pdb=" O VAL A1429 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A1431 " --> pdb=" O ASN A1375 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLU A1377 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A1428 " --> pdb=" O LEU A1454 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A1456 " --> pdb=" O THR A1428 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A1430 " --> pdb=" O LEU A1456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 26 removed outlier: 3.679A pdb=" N ILE C 55 " --> pdb=" O TRP C 34 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 822 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: 0.65 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2054 1.34 - 1.46: 1443 1.46 - 1.58: 3107 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 6641 Sorted by residual: bond pdb=" C PRO A1188 " pdb=" N GLU A1189 " ideal model delta sigma weight residual 1.333 1.378 -0.045 2.74e-02 1.33e+03 2.74e+00 bond pdb=" C TYR C 61 " pdb=" N PRO C 62 " ideal model delta sigma weight residual 1.337 1.348 -0.011 1.06e-02 8.90e+03 1.15e+00 bond pdb=" CG LEU A1186 " pdb=" CD2 LEU A1186 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 bond pdb=" CB ARG A1163 " pdb=" CG ARG A1163 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.50e-01 bond pdb=" CB LEU A1186 " pdb=" CG LEU A1186 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.07e-01 ... (remaining 6636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 8824 1.75 - 3.49: 148 3.49 - 5.24: 10 5.24 - 6.98: 3 6.98 - 8.73: 3 Bond angle restraints: 8988 Sorted by residual: angle pdb=" C HIS A 820 " pdb=" N ASP A 821 " pdb=" CA ASP A 821 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C ASP C 60 " pdb=" N TYR C 61 " pdb=" CA TYR C 61 " ideal model delta sigma weight residual 120.58 125.11 -4.53 1.32e+00 5.74e-01 1.18e+01 angle pdb=" N CYS A1450 " pdb=" CA CYS A1450 " pdb=" C CYS A1450 " ideal model delta sigma weight residual 111.03 107.83 3.20 1.11e+00 8.12e-01 8.30e+00 angle pdb=" C VAL A1447 " pdb=" N MET A1448 " pdb=" CA MET A1448 " ideal model delta sigma weight residual 122.08 126.22 -4.14 1.47e+00 4.63e-01 7.94e+00 angle pdb=" CA LEU A1186 " pdb=" CB LEU A1186 " pdb=" CG LEU A1186 " ideal model delta sigma weight residual 116.30 125.03 -8.73 3.50e+00 8.16e-02 6.22e+00 ... (remaining 8983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 3595 15.08 - 30.15: 272 30.15 - 45.23: 75 45.23 - 60.30: 26 60.30 - 75.37: 5 Dihedral angle restraints: 3973 sinusoidal: 1578 harmonic: 2395 Sorted by residual: dihedral pdb=" CA ALA C 139 " pdb=" C ALA C 139 " pdb=" N ARG C 140 " pdb=" CA ARG C 140 " ideal model delta harmonic sigma weight residual -180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLY A1068 " pdb=" C GLY A1068 " pdb=" N TYR A1069 " pdb=" CA TYR A1069 " ideal model delta harmonic sigma weight residual 180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU A1185 " pdb=" C LEU A1185 " pdb=" N LEU A1186 " pdb=" CA LEU A1186 " ideal model delta harmonic sigma weight residual 180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 506 0.025 - 0.050: 312 0.050 - 0.075: 128 0.075 - 0.101: 50 0.101 - 0.126: 26 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA ILE A1297 " pdb=" N ILE A1297 " pdb=" C ILE A1297 " pdb=" CB ILE A1297 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL A1244 " pdb=" N VAL A1244 " pdb=" C VAL A1244 " pdb=" CB VAL A1244 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA ILE A 834 " pdb=" N ILE A 834 " pdb=" C ILE A 834 " pdb=" CB ILE A 834 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1019 not shown) Planarity restraints: 1136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1424 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A1425 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1425 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1425 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 95 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 96 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1238 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A1239 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1239 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1239 " -0.016 5.00e-02 4.00e+02 ... (remaining 1133 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 6984 3.28 - 3.82: 11062 3.82 - 4.36: 12761 4.36 - 4.90: 21116 Nonbonded interactions: 52632 Sorted by model distance: nonbonded pdb=" O GLU A1435 " pdb=" OH TYR A1443 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.233 3.040 nonbonded pdb=" OE1 GLU A1256 " pdb=" NZ LYS A1267 " model vdw 2.242 3.120 nonbonded pdb=" O PRO A1054 " pdb=" OG1 THR A1057 " model vdw 2.243 3.040 nonbonded pdb=" OG SER C 23 " pdb=" OG SER C 37 " model vdw 2.249 3.040 ... (remaining 52627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 1.120 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: 0.020 Set scattering table: 0.020 Process input model: 6.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.004 0.045 6641 Z= 0.183 Angle : 0.566 8.728 8988 Z= 0.308 Chirality : 0.041 0.126 1022 Planarity : 0.004 0.048 1136 Dihedral : 12.837 75.375 2417 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 6.09 % Allowed : 8.02 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.31), residues: 805 helix: 0.99 (0.27), residues: 395 sheet: -0.04 (0.73), residues: 50 loop : -0.67 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1163 TYR 0.008 0.001 TYR A1147 PHE 0.014 0.002 PHE A1229 TRP 0.009 0.001 TRP A1365 HIS 0.003 0.001 HIS A1378 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6641) covalent geometry : angle 0.56565 ( 8988) hydrogen bonds : bond 0.15698 ( 283) hydrogen bonds : angle 5.62388 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1009 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5828 (m) REVERT: A 1022 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8436 (ttpt) REVERT: A 1029 GLU cc_start: 0.7648 (tp30) cc_final: 0.6926 (tm-30) REVERT: A 1058 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7308 (mtm110) REVERT: A 1115 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 1185 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6455 (pp) REVERT: A 1220 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7457 (pp) REVERT: A 1349 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.6087 (mm) REVERT: A 1370 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.7006 (mt) REVERT: A 1389 ASP cc_start: 0.7890 (m-30) cc_final: 0.7551 (m-30) REVERT: A 1423 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7588 (tt) REVERT: A 1427 PHE cc_start: 0.7783 (t80) cc_final: 0.7580 (t80) REVERT: C 9 LYS cc_start: 0.8411 (tmtt) cc_final: 0.7980 (tptp) outliers start: 44 outliers final: 16 residues processed: 136 average time/residue: 0.0930 time to fit residues: 16.4514 Evaluate side-chains 97 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 928 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1012 ASP Chi-restraints excluded: chain A residue 1058 ARG Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1204 PHE Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1352 ASP Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095021 restraints weight = 14361.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.098770 restraints weight = 7602.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.101215 restraints weight = 5139.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.102614 restraints weight = 4019.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103357 restraints weight = 3475.034| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6641 Z= 0.120 Angle : 0.543 6.471 8988 Z= 0.282 Chirality : 0.041 0.156 1022 Planarity : 0.004 0.043 1136 Dihedral : 7.699 59.546 920 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.56 % Allowed : 9.96 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.29 (0.30), residues: 805 helix: 0.89 (0.26), residues: 416 sheet: 0.39 (0.75), residues: 48 loop : -0.64 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1163 TYR 0.011 0.001 TYR A1069 PHE 0.017 0.001 PHE A1337 TRP 0.009 0.001 TRP A 946 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6641) covalent geometry : angle 0.54258 ( 8988) hydrogen bonds : bond 0.03703 ( 283) hydrogen bonds : angle 4.52301 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.211 Fit side-chains REVERT: A 928 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 1009 VAL cc_start: 0.6355 (OUTLIER) cc_final: 0.6009 (m) REVERT: A 1029 GLU cc_start: 0.7776 (tp30) cc_final: 0.7097 (tm-30) REVERT: A 1185 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6821 (pp) REVERT: A 1220 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7515 (pp) REVERT: A 1276 ASN cc_start: 0.6337 (t0) cc_final: 0.6058 (t0) REVERT: A 1279 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 1389 ASP cc_start: 0.7857 (m-30) cc_final: 0.7515 (m-30) REVERT: A 1423 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7611 (tt) REVERT: C 13 ASP cc_start: 0.8656 (m-30) cc_final: 0.8362 (m-30) outliers start: 33 outliers final: 15 residues processed: 119 average time/residue: 0.0816 time to fit residues: 12.7623 Evaluate side-chains 94 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 928 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1352 ASP Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096328 restraints weight = 14242.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.100108 restraints weight = 7478.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.102530 restraints weight = 5038.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.104045 restraints weight = 3933.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104846 restraints weight = 3381.119| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6641 Z= 0.109 Angle : 0.538 8.368 8988 Z= 0.272 Chirality : 0.040 0.151 1022 Planarity : 0.004 0.041 1136 Dihedral : 6.187 57.444 895 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.01 % Allowed : 12.45 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.30), residues: 805 helix: 1.04 (0.26), residues: 411 sheet: -0.16 (0.67), residues: 57 loop : -0.56 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1101 TYR 0.013 0.001 TYR A1069 PHE 0.014 0.001 PHE A1427 TRP 0.007 0.001 TRP A1076 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6641) covalent geometry : angle 0.53845 ( 8988) hydrogen bonds : bond 0.03352 ( 283) hydrogen bonds : angle 4.35610 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 928 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 1009 VAL cc_start: 0.6055 (OUTLIER) cc_final: 0.5754 (m) REVERT: A 1029 GLU cc_start: 0.7811 (tp30) cc_final: 0.7134 (tm-30) REVERT: A 1045 LEU cc_start: 0.8021 (mt) cc_final: 0.7788 (mt) REVERT: A 1220 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7521 (pp) REVERT: A 1279 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 1389 ASP cc_start: 0.7692 (m-30) cc_final: 0.7456 (m-30) REVERT: A 1423 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7665 (tt) REVERT: C 13 ASP cc_start: 0.8676 (m-30) cc_final: 0.8442 (m-30) outliers start: 29 outliers final: 15 residues processed: 112 average time/residue: 0.0690 time to fit residues: 10.4248 Evaluate side-chains 91 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 928 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1352 ASP Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.129059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.095064 restraints weight = 14310.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.098688 restraints weight = 7662.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.101041 restraints weight = 5195.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102571 restraints weight = 4062.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.103387 restraints weight = 3472.108| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6641 Z= 0.127 Angle : 0.558 7.646 8988 Z= 0.276 Chirality : 0.042 0.273 1022 Planarity : 0.004 0.041 1136 Dihedral : 5.935 53.591 892 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.15 % Allowed : 13.83 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.31 (0.30), residues: 805 helix: 0.91 (0.26), residues: 416 sheet: -0.04 (0.67), residues: 57 loop : -0.57 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1101 TYR 0.014 0.001 TYR A1206 PHE 0.016 0.001 PHE A1427 TRP 0.009 0.001 TRP A1162 HIS 0.004 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6641) covalent geometry : angle 0.55781 ( 8988) hydrogen bonds : bond 0.03318 ( 283) hydrogen bonds : angle 4.28826 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 1009 VAL cc_start: 0.6204 (OUTLIER) cc_final: 0.5896 (m) REVERT: A 1029 GLU cc_start: 0.7881 (tp30) cc_final: 0.7325 (tp30) REVERT: A 1185 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6521 (pp) REVERT: A 1220 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7476 (pp) REVERT: A 1276 ASN cc_start: 0.6922 (t0) cc_final: 0.6208 (t0) REVERT: A 1279 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 1423 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7626 (tt) REVERT: C 5 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8794 (tmmt) REVERT: C 13 ASP cc_start: 0.8721 (m-30) cc_final: 0.8429 (m-30) REVERT: C 145 LYS cc_start: 0.8823 (pttm) cc_final: 0.8581 (pttm) outliers start: 30 outliers final: 19 residues processed: 108 average time/residue: 0.0750 time to fit residues: 10.6725 Evaluate side-chains 93 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.128839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.094968 restraints weight = 14195.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098401 restraints weight = 7751.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100641 restraints weight = 5332.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102144 restraints weight = 4199.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103066 restraints weight = 3613.418| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6641 Z= 0.120 Angle : 0.545 7.350 8988 Z= 0.272 Chirality : 0.041 0.154 1022 Planarity : 0.004 0.039 1136 Dihedral : 5.319 52.019 885 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.29 % Allowed : 14.66 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.33 (0.30), residues: 805 helix: 0.95 (0.26), residues: 417 sheet: -0.02 (0.67), residues: 57 loop : -0.60 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1101 TYR 0.012 0.001 TYR A1206 PHE 0.016 0.001 PHE A1061 TRP 0.006 0.001 TRP A1076 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6641) covalent geometry : angle 0.54469 ( 8988) hydrogen bonds : bond 0.03222 ( 283) hydrogen bonds : angle 4.21745 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: A 1009 VAL cc_start: 0.6281 (OUTLIER) cc_final: 0.5957 (m) REVERT: A 1029 GLU cc_start: 0.7870 (tp30) cc_final: 0.7538 (tp30) REVERT: A 1185 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6745 (pp) REVERT: A 1220 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 1279 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8081 (mm) REVERT: A 1382 MET cc_start: 0.7234 (tpp) cc_final: 0.6763 (tpp) REVERT: A 1423 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7640 (tt) REVERT: C 13 ASP cc_start: 0.8672 (m-30) cc_final: 0.8429 (m-30) outliers start: 31 outliers final: 18 residues processed: 102 average time/residue: 0.0775 time to fit residues: 10.5498 Evaluate side-chains 86 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 chunk 6 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.128350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094430 restraints weight = 14309.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.097997 restraints weight = 7648.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100305 restraints weight = 5195.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101778 restraints weight = 4071.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.102523 restraints weight = 3501.015| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6641 Z= 0.143 Angle : 0.580 11.111 8988 Z= 0.284 Chirality : 0.042 0.156 1022 Planarity : 0.004 0.040 1136 Dihedral : 5.428 54.162 885 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.43 % Allowed : 14.80 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.18 (0.30), residues: 805 helix: 0.81 (0.25), residues: 423 sheet: -0.07 (0.67), residues: 57 loop : -0.67 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.014 0.001 TYR C 75 PHE 0.018 0.002 PHE A1053 TRP 0.008 0.001 TRP A1162 HIS 0.004 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6641) covalent geometry : angle 0.57956 ( 8988) hydrogen bonds : bond 0.03324 ( 283) hydrogen bonds : angle 4.30045 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6156 (pm20) REVERT: A 1009 VAL cc_start: 0.6132 (OUTLIER) cc_final: 0.5793 (m) REVERT: A 1029 GLU cc_start: 0.7952 (tp30) cc_final: 0.7583 (tp30) REVERT: A 1185 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6763 (pp) REVERT: A 1220 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7484 (pp) REVERT: A 1276 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 1279 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 1382 MET cc_start: 0.7291 (tpp) cc_final: 0.6822 (tpp) REVERT: A 1423 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7635 (tt) REVERT: C 13 ASP cc_start: 0.8699 (m-30) cc_final: 0.8425 (m-30) outliers start: 32 outliers final: 21 residues processed: 95 average time/residue: 0.0825 time to fit residues: 10.5757 Evaluate side-chains 88 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.130333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096347 restraints weight = 14114.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.099978 restraints weight = 7541.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102348 restraints weight = 5110.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103866 restraints weight = 4004.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104668 restraints weight = 3437.600| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6641 Z= 0.107 Angle : 0.566 10.136 8988 Z= 0.275 Chirality : 0.041 0.233 1022 Planarity : 0.003 0.038 1136 Dihedral : 5.368 56.238 885 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.15 % Allowed : 15.21 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: 0.37 (0.30), residues: 805 helix: 0.95 (0.26), residues: 419 sheet: -0.05 (0.67), residues: 57 loop : -0.53 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 140 TYR 0.013 0.001 TYR A1371 PHE 0.030 0.001 PHE A1061 TRP 0.006 0.001 TRP A1162 HIS 0.004 0.001 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6641) covalent geometry : angle 0.56584 ( 8988) hydrogen bonds : bond 0.03115 ( 283) hydrogen bonds : angle 4.16722 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6177 (pm20) REVERT: A 1009 VAL cc_start: 0.6153 (OUTLIER) cc_final: 0.5836 (m) REVERT: A 1029 GLU cc_start: 0.7987 (tp30) cc_final: 0.7528 (tp30) REVERT: A 1185 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6696 (pp) REVERT: A 1220 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7453 (pp) REVERT: A 1276 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 1279 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 1382 MET cc_start: 0.7305 (tpp) cc_final: 0.6862 (tpp) REVERT: A 1423 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7599 (tt) REVERT: C 13 ASP cc_start: 0.8709 (m-30) cc_final: 0.8414 (m-30) outliers start: 30 outliers final: 18 residues processed: 99 average time/residue: 0.0705 time to fit residues: 9.4834 Evaluate side-chains 93 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.129881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.095515 restraints weight = 14287.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.099146 restraints weight = 7621.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.101520 restraints weight = 5178.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.103003 restraints weight = 4055.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103913 restraints weight = 3482.540| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6641 Z= 0.119 Angle : 0.581 10.903 8988 Z= 0.285 Chirality : 0.042 0.273 1022 Planarity : 0.003 0.039 1136 Dihedral : 5.430 57.708 884 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.01 % Allowed : 15.63 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: 0.37 (0.30), residues: 805 helix: 0.94 (0.26), residues: 419 sheet: -0.00 (0.67), residues: 57 loop : -0.53 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.012 0.001 TYR A1371 PHE 0.033 0.001 PHE A1061 TRP 0.006 0.001 TRP A1162 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6641) covalent geometry : angle 0.58144 ( 8988) hydrogen bonds : bond 0.03115 ( 283) hydrogen bonds : angle 4.16607 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: A 1009 VAL cc_start: 0.6091 (OUTLIER) cc_final: 0.5780 (m) REVERT: A 1029 GLU cc_start: 0.7967 (tp30) cc_final: 0.7491 (tp30) REVERT: A 1185 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6671 (pp) REVERT: A 1220 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7465 (pp) REVERT: A 1279 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 1282 LEU cc_start: 0.8580 (tt) cc_final: 0.8071 (tt) REVERT: A 1284 LEU cc_start: 0.8257 (mm) cc_final: 0.7843 (tp) REVERT: A 1382 MET cc_start: 0.7407 (tpp) cc_final: 0.6979 (tpp) REVERT: A 1423 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7593 (tt) REVERT: C 13 ASP cc_start: 0.8706 (m-30) cc_final: 0.8386 (m-30) REVERT: C 140 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8022 (mmt-90) outliers start: 29 outliers final: 21 residues processed: 96 average time/residue: 0.0753 time to fit residues: 9.7692 Evaluate side-chains 91 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1204 PHE Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.130863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096585 restraints weight = 14456.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.100350 restraints weight = 7591.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.102789 restraints weight = 5101.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104361 restraints weight = 3970.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105178 restraints weight = 3415.218| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6641 Z= 0.114 Angle : 0.580 11.234 8988 Z= 0.284 Chirality : 0.042 0.280 1022 Planarity : 0.003 0.039 1136 Dihedral : 5.388 59.222 884 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.87 % Allowed : 16.18 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.30), residues: 805 helix: 0.97 (0.26), residues: 419 sheet: -0.41 (0.64), residues: 69 loop : -0.44 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1101 TYR 0.012 0.001 TYR C 75 PHE 0.029 0.001 PHE A1061 TRP 0.006 0.001 TRP A1076 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6641) covalent geometry : angle 0.58022 ( 8988) hydrogen bonds : bond 0.02980 ( 283) hydrogen bonds : angle 4.13797 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: A 1009 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5847 (m) REVERT: A 1029 GLU cc_start: 0.7986 (tp30) cc_final: 0.7552 (tp30) REVERT: A 1185 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6645 (pp) REVERT: A 1220 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7459 (pp) REVERT: A 1279 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 1282 LEU cc_start: 0.8624 (tt) cc_final: 0.8270 (tt) REVERT: A 1284 LEU cc_start: 0.8239 (mm) cc_final: 0.7920 (tp) REVERT: A 1382 MET cc_start: 0.7425 (tpp) cc_final: 0.6995 (tpp) REVERT: A 1423 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7521 (tt) REVERT: C 13 ASP cc_start: 0.8691 (m-30) cc_final: 0.8335 (m-30) REVERT: C 39 MET cc_start: 0.7898 (mmm) cc_final: 0.7158 (ppp) outliers start: 28 outliers final: 21 residues processed: 93 average time/residue: 0.0703 time to fit residues: 8.7998 Evaluate side-chains 89 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1204 PHE Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1234 HIS Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095333 restraints weight = 14020.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.098866 restraints weight = 7535.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101121 restraints weight = 5118.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102506 restraints weight = 4026.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103469 restraints weight = 3473.988| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6641 Z= 0.128 Angle : 0.584 11.148 8988 Z= 0.286 Chirality : 0.042 0.284 1022 Planarity : 0.003 0.039 1136 Dihedral : 5.396 55.951 884 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.73 % Allowed : 16.46 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.34 (0.30), residues: 805 helix: 0.93 (0.26), residues: 419 sheet: -0.43 (0.64), residues: 69 loop : -0.47 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 16 TYR 0.015 0.001 TYR C 75 PHE 0.028 0.001 PHE A1061 TRP 0.008 0.001 TRP A1076 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6641) covalent geometry : angle 0.58370 ( 8988) hydrogen bonds : bond 0.03040 ( 283) hydrogen bonds : angle 4.19236 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 716 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6137 (pm20) REVERT: A 1009 VAL cc_start: 0.6198 (OUTLIER) cc_final: 0.5880 (m) REVERT: A 1029 GLU cc_start: 0.7937 (tp30) cc_final: 0.7584 (tp30) REVERT: A 1185 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6666 (pp) REVERT: A 1220 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7485 (pp) REVERT: A 1279 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 1282 LEU cc_start: 0.8622 (tt) cc_final: 0.8311 (tt) REVERT: A 1284 LEU cc_start: 0.8229 (mm) cc_final: 0.7929 (tp) REVERT: A 1382 MET cc_start: 0.7410 (tpp) cc_final: 0.6969 (tpp) REVERT: A 1423 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7553 (tt) outliers start: 27 outliers final: 20 residues processed: 89 average time/residue: 0.0835 time to fit residues: 10.1927 Evaluate side-chains 89 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1415 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.128573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094468 restraints weight = 14181.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.098020 restraints weight = 7699.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.100300 restraints weight = 5253.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101625 restraints weight = 4130.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102609 restraints weight = 3581.364| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6641 Z= 0.139 Angle : 0.612 11.119 8988 Z= 0.297 Chirality : 0.042 0.275 1022 Planarity : 0.004 0.040 1136 Dihedral : 5.414 54.754 884 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.73 % Allowed : 16.87 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.34 (0.30), residues: 805 helix: 0.93 (0.26), residues: 418 sheet: -0.35 (0.68), residues: 62 loop : -0.48 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.025 0.001 TYR C 75 PHE 0.027 0.001 PHE A1061 TRP 0.008 0.001 TRP A1076 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6641) covalent geometry : angle 0.61218 ( 8988) hydrogen bonds : bond 0.03086 ( 283) hydrogen bonds : angle 4.23953 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.98 seconds wall clock time: 26 minutes 27.11 seconds (1587.11 seconds total)