Starting phenix.real_space_refine on Wed Aug 5 21:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.map" model { file = "/net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s2c_54488/08_2026/9s2c_54488.cif" } resolution = 2.9 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= 0.001 sd= 0.063 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 7402 2.51 5 N 1864 2.21 5 O 2077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11410 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 11092 Classifications: {'peptide': 1388} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1334} Chain breaks: 4 Chain: "A" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 318 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1, 'ERG': 8, 'VO4': 1} Classifications: {'undetermined': 12, 'water': 22} Link IDs: {None: 33} Time building chain proxies: 1.91, per 1000 atoms: 0.17 Number of scatterers: 11410 At special positions: 0 Unit cell: (92.29, 101.519, 149.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 60 16.00 P 5 15.00 Mg 1 11.99 O 2077 8.00 N 1864 7.00 C 7402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1399 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1415 " - pdb=" SG CYS A1440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 455.4 milliseconds 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2602 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 59.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.755A pdb=" N ASP A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.550A pdb=" N TYR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.667A pdb=" N THR A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.599A pdb=" N PHE A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 329 through 348 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.665A pdb=" N THR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 443 through 458 removed outlier: 3.725A pdb=" N ALA A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.526A pdb=" N LEU A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 508 through 531 removed outlier: 4.243A pdb=" N THR A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 543 through 562 removed outlier: 3.674A pdb=" N LEU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.538A pdb=" N LEU A 567 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 568 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 584 through 615 removed outlier: 3.750A pdb=" N ASP A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 589 " --> pdb=" O PRO A 585 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'A' and resid 620 through 648 removed outlier: 3.604A pdb=" N VAL A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.982A pdb=" N VAL A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.965A pdb=" N ILE A 686 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.865A pdb=" N TYR A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 745 through 753 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 759 through 784 removed outlier: 3.521A pdb=" N GLY A 763 " --> pdb=" O HIS A 759 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 808 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 948 through 961 Processing helix chain 'A' and resid 966 through 981 Processing helix chain 'A' and resid 999 through 1014 removed outlier: 3.712A pdb=" N ALA A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1084 through 1097 removed outlier: 3.940A pdb=" N CYS A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1117 removed outlier: 3.772A pdb=" N LEU A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1136 through 1158 removed outlier: 3.711A pdb=" N GLN A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) Proline residue: A1154 - end of helix Processing helix chain 'A' and resid 1171 through 1189 Processing helix chain 'A' and resid 1190 through 1212 removed outlier: 3.527A pdb=" N LEU A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1232 Processing helix chain 'A' and resid 1235 through 1257 Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1265 through 1291 Proline residue: A1279 - end of helix removed outlier: 3.849A pdb=" N ILE A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1305 Processing helix chain 'A' and resid 1307 through 1336 removed outlier: 4.541A pdb=" N PHE A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1371 through 1378 removed outlier: 3.559A pdb=" N TYR A1375 " --> pdb=" O TRP A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1393 removed outlier: 3.622A pdb=" N ASP A1385 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1393 " --> pdb=" O SER A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.802A pdb=" N PHE A1451 " --> pdb=" O HIS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1489 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 231 removed outlier: 6.610A pdb=" N GLN A 319 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA A 354 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TRP A 321 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 178 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 177 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS A 370 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 179 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 372 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 181 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 369 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 380 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 371 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 4.609A pdb=" N ILE A 417 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 708 through 710 Processing sheet with id=AA7, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AA8, first strand: chain 'A' and resid 874 through 883 removed outlier: 6.426A pdb=" N ILE A 875 " --> pdb=" O ASP A 865 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 865 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 877 " --> pdb=" O CYS A 863 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A 863 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL A 879 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A 862 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 916 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR A 864 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 914 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 935 through 937 removed outlier: 6.310A pdb=" N THR A 887 " --> pdb=" O ILE A1051 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS A1053 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 889 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A1068 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB2, first strand: chain 'A' and resid 1405 through 1407 603 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2227 1.33 - 1.47: 4382 1.47 - 1.62: 4991 1.62 - 1.76: 1 1.76 - 1.91: 96 Bond restraints: 11697 Sorted by residual: bond pdb=" C PRO A1154 " pdb=" O PRO A1154 " ideal model delta sigma weight residual 1.235 1.343 -0.108 1.30e-02 5.92e+03 6.86e+01 bond pdb=" C LEU A1153 " pdb=" O LEU A1153 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" N PRO A1154 " pdb=" CA PRO A1154 " ideal model delta sigma weight residual 1.469 1.420 0.049 1.28e-02 6.10e+03 1.44e+01 bond pdb=" CA SER A1150 " pdb=" CB SER A1150 " ideal model delta sigma weight residual 1.533 1.475 0.058 1.60e-02 3.91e+03 1.32e+01 bond pdb=" C LYS A1155 " pdb=" O LYS A1155 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.26e-02 6.30e+03 9.10e+00 ... (remaining 11692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15753 2.85 - 5.71: 146 5.71 - 8.56: 20 8.56 - 11.42: 4 11.42 - 14.27: 1 Bond angle restraints: 15924 Sorted by residual: angle pdb=" C ASN A1157 " pdb=" N THR A1158 " pdb=" CA THR A1158 " ideal model delta sigma weight residual 121.54 107.27 14.27 1.91e+00 2.74e-01 5.58e+01 angle pdb=" C PRO A1154 " pdb=" CA PRO A1154 " pdb=" CB PRO A1154 " ideal model delta sigma weight residual 111.56 101.42 10.14 1.65e+00 3.67e-01 3.78e+01 angle pdb=" CA GLU A1152 " pdb=" C GLU A1152 " pdb=" O GLU A1152 " ideal model delta sigma weight residual 120.55 114.47 6.08 1.07e+00 8.73e-01 3.23e+01 angle pdb=" N SER A1150 " pdb=" CA SER A1150 " pdb=" C SER A1150 " ideal model delta sigma weight residual 114.75 107.73 7.02 1.26e+00 6.30e-01 3.10e+01 angle pdb=" CA LEU A1153 " pdb=" C LEU A1153 " pdb=" O LEU A1153 " ideal model delta sigma weight residual 120.16 113.80 6.36 1.37e+00 5.33e-01 2.16e+01 ... (remaining 15919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6989 35.51 - 71.02: 286 71.02 - 106.53: 11 106.53 - 142.04: 0 142.04 - 177.55: 1 Dihedral angle restraints: 7287 sinusoidal: 3228 harmonic: 4059 Sorted by residual: dihedral pdb=" CB CYS A 711 " pdb=" SG CYS A 711 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -150.09 64.09 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" C2' ADP A1604 " pdb=" C1' ADP A1604 " pdb=" N9 ADP A1604 " pdb=" C4 ADP A1604 " ideal model delta sinusoidal sigma weight residual 91.55 -86.00 177.55 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C PRO A1154 " pdb=" N PRO A1154 " pdb=" CA PRO A1154 " pdb=" CB PRO A1154 " ideal model delta harmonic sigma weight residual -120.70 -105.78 -14.92 0 2.50e+00 1.60e-01 3.56e+01 ... (remaining 7284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1381 0.052 - 0.103: 318 0.103 - 0.155: 51 0.155 - 0.207: 0 0.207 - 0.258: 3 Chirality restraints: 1753 Sorted by residual: chirality pdb=" C20 ERG A1606 " pdb=" C17 ERG A1606 " pdb=" C21 ERG A1606 " pdb=" C22 ERG A1606 " both_signs ideal model delta sigma weight residual False 2.58 2.32 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PRO A1154 " pdb=" N PRO A1154 " pdb=" C PRO A1154 " pdb=" CB PRO A1154 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A1055 " pdb=" CA ILE A1055 " pdb=" CG1 ILE A1055 " pdb=" CG2 ILE A1055 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1750 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1154 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PRO A1154 " -0.066 2.00e-02 2.50e+03 pdb=" O PRO A1154 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A1155 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1153 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LEU A1153 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A1153 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A1154 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1158 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C THR A1158 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A1158 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A1159 " -0.018 2.00e-02 2.50e+03 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 102 2.58 - 3.16: 9461 3.16 - 3.74: 18318 3.74 - 4.32: 26201 4.32 - 4.90: 43122 Nonbonded interactions: 97204 Sorted by model distance: nonbonded pdb=" O4 VO4 A1602 " pdb="MG MG A1603 " model vdw 1.997 2.170 nonbonded pdb=" OH TYR A 669 " pdb=" OG1 THR A1211 " model vdw 2.095 3.040 nonbonded pdb=" OH TYR A 395 " pdb=" O PRO A 430 " model vdw 2.181 3.040 nonbonded pdb=" O ARG A1257 " pdb=" OG SER A1261 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR A 900 " pdb="MG MG A1603 " model vdw 2.222 2.170 ... (remaining 97199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 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 : 0.005 0.108 11701 Z= 0.242 Angle : 0.732 14.274 15930 Z= 0.393 Chirality : 0.044 0.258 1753 Planarity : 0.005 0.042 1969 Dihedral : 17.325 177.551 4676 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.64 % Favored : 95.07 % Rotamer: Outliers : 2.42 % Allowed : 24.64 % Favored : 72.93 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1378 helix: 1.26 (0.19), residues: 756 sheet: -1.17 (0.57), residues: 80 loop : -1.25 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 804 TYR 0.020 0.002 TYR A 936 PHE 0.025 0.002 PHE A1203 TRP 0.034 0.002 TRP A 687 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (11697) covalent geometry : angle 0.73232 / 0.39 (15924) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 0.57239 / 0.29 ( 6) hydrogen bonds : bond 0.13762 / 8.84 ( 603) hydrogen bonds : angle 6.10020 / 4.31 ( 1749) Misc. bond : bond 0.00442 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.323 Fit side-chains REVERT: A 129 ILE cc_start: 0.8708 (mp) cc_final: 0.8361 (mt) REVERT: A 451 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8127 (ttpp) REVERT: A 479 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7375 (ttt180) REVERT: A 507 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6220 (mp10) REVERT: A 513 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 528 SER cc_start: 0.8811 (t) cc_final: 0.8475 (p) REVERT: A 596 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 625 PHE cc_start: 0.7417 (m-10) cc_final: 0.6447 (t80) REVERT: A 688 TYR cc_start: 0.8085 (m-80) cc_final: 0.7734 (m-80) REVERT: A 804 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7368 (tmm-80) REVERT: A 985 GLN cc_start: 0.8743 (tp40) cc_final: 0.7792 (mp10) REVERT: A 1056 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.7525 (t-90) REVERT: A 1137 ASP cc_start: 0.8103 (t70) cc_final: 0.7902 (t0) REVERT: A 1363 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7765 (p) outliers start: 29 outliers final: 18 residues processed: 144 average time/residue: 0.4960 time to fit residues: 77.5960 Evaluate side-chains 131 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1363 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 759 HIS A1064 GLN A1157 ASN A1175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115424 restraints weight = 13598.554| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.72 r_work: 0.3150 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11701 Z= 0.159 Angle : 0.608 14.899 15930 Z= 0.297 Chirality : 0.042 0.248 1753 Planarity : 0.004 0.048 1969 Dihedral : 10.278 178.319 2143 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 4.18 % Allowed : 22.39 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1378 helix: 1.60 (0.18), residues: 782 sheet: -1.22 (0.57), residues: 80 loop : -1.10 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 676 TYR 0.014 0.001 TYR A 936 PHE 0.022 0.002 PHE A 774 TRP 0.030 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11697) covalent geometry : angle 0.60787 / 0.30 (15924) SS BOND : bond 0.00175 / 0.09 ( 3) SS BOND : angle 1.04858 / 0.59 ( 6) hydrogen bonds : bond 0.04886 / 3.17 ( 603) hydrogen bonds : angle 4.51071 / 3.20 ( 1749) Misc. bond : bond 0.00441 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.252 Fit side-chains REVERT: A 129 ILE cc_start: 0.8702 (mp) cc_final: 0.8369 (mt) REVERT: A 392 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8208 (mtmm) REVERT: A 451 LYS cc_start: 0.8318 (ttpp) cc_final: 0.8072 (ttpp) REVERT: A 479 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7336 (ttt180) REVERT: A 507 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6231 (mp10) REVERT: A 528 SER cc_start: 0.8837 (t) cc_final: 0.8523 (p) REVERT: A 596 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 625 PHE cc_start: 0.7372 (m-10) cc_final: 0.6424 (t80) REVERT: A 804 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7437 (tmm-80) REVERT: A 979 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8342 (tttp) REVERT: A 985 GLN cc_start: 0.8737 (tp40) cc_final: 0.7751 (mp10) REVERT: A 1296 ILE cc_start: 0.3283 (OUTLIER) cc_final: 0.2982 (mp) outliers start: 50 outliers final: 15 residues processed: 157 average time/residue: 0.4317 time to fit residues: 73.9534 Evaluate side-chains 129 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 132 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 GLN A1064 GLN A1242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115589 restraints weight = 13698.064| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.74 r_work: 0.3153 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11701 Z= 0.140 Angle : 0.572 13.713 15930 Z= 0.278 Chirality : 0.041 0.248 1753 Planarity : 0.004 0.039 1969 Dihedral : 9.884 179.988 2121 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 4.51 % Allowed : 21.47 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1378 helix: 1.78 (0.19), residues: 782 sheet: -1.27 (0.59), residues: 80 loop : -1.12 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1369 TYR 0.013 0.001 TYR A 936 PHE 0.018 0.001 PHE A 774 TRP 0.024 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11697) covalent geometry : angle 0.57178 / 0.28 (15924) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.72842 / 0.39 ( 6) hydrogen bonds : bond 0.04470 / 2.90 ( 603) hydrogen bonds : angle 4.31257 / 3.07 ( 1749) Misc. bond : bond 0.00420 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 392 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: A 451 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8041 (ttpp) REVERT: A 479 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7344 (ttt180) REVERT: A 507 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: A 528 SER cc_start: 0.8806 (t) cc_final: 0.8493 (p) REVERT: A 549 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7972 (mtt) REVERT: A 596 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 625 PHE cc_start: 0.7402 (m-10) cc_final: 0.6391 (t80) REVERT: A 804 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7377 (tmm-80) REVERT: A 979 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8298 (tttm) REVERT: A 985 GLN cc_start: 0.8739 (tp40) cc_final: 0.7748 (mp10) REVERT: A 1296 ILE cc_start: 0.3384 (OUTLIER) cc_final: 0.3113 (mp) REVERT: A 1363 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7739 (p) outliers start: 54 outliers final: 22 residues processed: 161 average time/residue: 0.4537 time to fit residues: 79.9169 Evaluate side-chains 141 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115940 restraints weight = 13634.948| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.80 r_work: 0.3143 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11701 Z= 0.145 Angle : 0.569 13.142 15930 Z= 0.278 Chirality : 0.042 0.251 1753 Planarity : 0.004 0.039 1969 Dihedral : 9.839 179.911 2121 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 5.01 % Allowed : 21.39 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.23), residues: 1378 helix: 1.83 (0.19), residues: 782 sheet: -1.24 (0.59), residues: 80 loop : -1.13 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1369 TYR 0.014 0.001 TYR A1129 PHE 0.019 0.001 PHE A 774 TRP 0.024 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11697) covalent geometry : angle 0.56939 / 0.28 (15924) SS BOND : bond 0.00147 / 0.07 ( 3) SS BOND : angle 0.60564 / 0.30 ( 6) hydrogen bonds : bond 0.04429 / 2.89 ( 603) hydrogen bonds : angle 4.24382 / 3.02 ( 1749) Misc. bond : bond 0.00426 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 0.326 Fit side-chains REVERT: A 129 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 274 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 392 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: A 451 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7961 (ttpp) REVERT: A 479 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7339 (ttt180) REVERT: A 507 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6239 (mp10) REVERT: A 528 SER cc_start: 0.8804 (t) cc_final: 0.8442 (p) REVERT: A 549 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7906 (mtt) REVERT: A 596 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: A 625 PHE cc_start: 0.7421 (m-10) cc_final: 0.6318 (t80) REVERT: A 804 ARG cc_start: 0.7699 (ttp80) cc_final: 0.6926 (tmm-80) REVERT: A 808 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6334 (mt-10) REVERT: A 940 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: A 979 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8218 (tttm) REVERT: A 985 GLN cc_start: 0.8698 (tp40) cc_final: 0.7668 (mp10) REVERT: A 1073 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: A 1296 ILE cc_start: 0.3203 (OUTLIER) cc_final: 0.2903 (mp) REVERT: A 1363 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7695 (p) outliers start: 60 outliers final: 23 residues processed: 162 average time/residue: 0.4227 time to fit residues: 74.9567 Evaluate side-chains 147 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 148 ASN A 420 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115520 restraints weight = 13633.371| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.80 r_work: 0.3130 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11701 Z= 0.152 Angle : 0.574 12.610 15930 Z= 0.281 Chirality : 0.042 0.254 1753 Planarity : 0.004 0.040 1969 Dihedral : 9.786 179.836 2118 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 5.43 % Allowed : 20.47 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1378 helix: 1.81 (0.19), residues: 783 sheet: -1.27 (0.59), residues: 80 loop : -1.14 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 729 TYR 0.015 0.001 TYR A1129 PHE 0.020 0.002 PHE A1203 TRP 0.024 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11697) covalent geometry : angle 0.57408 / 0.28 (15924) SS BOND : bond 0.00150 / 0.08 ( 3) SS BOND : angle 0.57373 / 0.27 ( 6) hydrogen bonds : bond 0.04434 / 2.89 ( 603) hydrogen bonds : angle 4.22156 / 3.00 ( 1749) Misc. bond : bond 0.00429 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 0.269 Fit side-chains REVERT: A 129 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 144 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.6198 (mttp) REVERT: A 274 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 392 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (mtmm) REVERT: A 451 LYS cc_start: 0.8275 (ttpp) cc_final: 0.8024 (ttpp) REVERT: A 479 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7423 (ttt180) REVERT: A 507 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: A 528 SER cc_start: 0.8818 (t) cc_final: 0.8480 (p) REVERT: A 549 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7986 (mtt) REVERT: A 596 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: A 660 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8145 (p) REVERT: A 808 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: A 979 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8302 (tttm) REVERT: A 985 GLN cc_start: 0.8738 (tp40) cc_final: 0.7721 (mp10) REVERT: A 1073 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: A 1296 ILE cc_start: 0.3378 (OUTLIER) cc_final: 0.3094 (mp) REVERT: A 1363 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7752 (p) outliers start: 65 outliers final: 29 residues processed: 164 average time/residue: 0.4109 time to fit residues: 73.8399 Evaluate side-chains 155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115453 restraints weight = 13595.617| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.74 r_work: 0.3131 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11701 Z= 0.159 Angle : 0.577 12.206 15930 Z= 0.282 Chirality : 0.042 0.257 1753 Planarity : 0.004 0.040 1969 Dihedral : 9.809 179.274 2118 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 5.01 % Allowed : 20.97 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1378 helix: 1.79 (0.19), residues: 783 sheet: -1.32 (0.59), residues: 80 loop : -1.16 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 803 TYR 0.015 0.001 TYR A1129 PHE 0.022 0.002 PHE A1203 TRP 0.026 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (11697) covalent geometry : angle 0.57653 / 0.28 (15924) SS BOND : bond 0.00169 / 0.09 ( 3) SS BOND : angle 0.60914 / 0.28 ( 6) hydrogen bonds : bond 0.04492 / 2.92 ( 603) hydrogen bonds : angle 4.21297 / 2.99 ( 1749) Misc. bond : bond 0.00433 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 114 time to evaluate : 0.324 Fit side-chains REVERT: A 129 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8399 (mt) REVERT: A 274 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 392 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (mtmm) REVERT: A 451 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7998 (ttpp) REVERT: A 479 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7423 (ttt180) REVERT: A 507 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: A 528 SER cc_start: 0.8821 (t) cc_final: 0.8488 (p) REVERT: A 549 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: A 596 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 793 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: A 808 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6297 (mt-10) REVERT: A 979 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8306 (tttm) REVERT: A 985 GLN cc_start: 0.8747 (tp40) cc_final: 0.7734 (mp10) REVERT: A 1073 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: A 1253 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8239 (tm) REVERT: A 1296 ILE cc_start: 0.3462 (OUTLIER) cc_final: 0.3185 (mp) REVERT: A 1363 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7809 (p) outliers start: 60 outliers final: 30 residues processed: 161 average time/residue: 0.3976 time to fit residues: 70.3503 Evaluate side-chains 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 119 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114695 restraints weight = 13533.004| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.76 r_work: 0.3122 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11701 Z= 0.180 Angle : 0.595 12.036 15930 Z= 0.292 Chirality : 0.043 0.262 1753 Planarity : 0.004 0.041 1969 Dihedral : 9.885 178.609 2118 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 5.01 % Allowed : 21.39 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1378 helix: 1.74 (0.18), residues: 782 sheet: -1.42 (0.58), residues: 80 loop : -1.17 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 729 TYR 0.016 0.002 TYR A1129 PHE 0.022 0.002 PHE A1203 TRP 0.030 0.001 TRP A 687 HIS 0.004 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (11697) covalent geometry : angle 0.59519 / 0.29 (15924) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.66700 / 0.31 ( 6) hydrogen bonds : bond 0.04686 / 3.05 ( 603) hydrogen bonds : angle 4.24888 / 3.02 ( 1749) Misc. bond : bond 0.00443 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 0.278 Fit side-chains REVERT: A 129 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 207 GLU cc_start: 0.8261 (mp0) cc_final: 0.7931 (pp20) REVERT: A 274 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 392 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8249 (mtmm) REVERT: A 451 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7995 (ttpp) REVERT: A 479 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7412 (ttt180) REVERT: A 507 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6196 (mp10) REVERT: A 528 SER cc_start: 0.8847 (t) cc_final: 0.8508 (p) REVERT: A 549 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: A 596 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: A 660 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 793 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.6547 (mm-30) REVERT: A 808 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: A 985 GLN cc_start: 0.8754 (tp40) cc_final: 0.7726 (mp10) REVERT: A 1073 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: A 1253 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8233 (tm) REVERT: A 1296 ILE cc_start: 0.3520 (OUTLIER) cc_final: 0.3219 (mp) REVERT: A 1363 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7828 (p) outliers start: 60 outliers final: 30 residues processed: 159 average time/residue: 0.4447 time to fit residues: 77.6765 Evaluate side-chains 152 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113528 restraints weight = 13557.318| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.82 r_work: 0.3099 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11701 Z= 0.196 Angle : 0.611 11.932 15930 Z= 0.300 Chirality : 0.044 0.266 1753 Planarity : 0.004 0.041 1969 Dihedral : 9.975 178.125 2118 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.43 % Allowed : 21.55 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1378 helix: 1.69 (0.18), residues: 780 sheet: -1.53 (0.58), residues: 80 loop : -1.19 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 729 TYR 0.017 0.002 TYR A1129 PHE 0.023 0.002 PHE A1203 TRP 0.037 0.001 TRP A 687 HIS 0.004 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (11697) covalent geometry : angle 0.61106 / 0.30 (15924) SS BOND : bond 0.00208 / 0.11 ( 3) SS BOND : angle 0.73242 / 0.33 ( 6) hydrogen bonds : bond 0.04851 / 3.16 ( 603) hydrogen bonds : angle 4.28688 / 3.04 ( 1749) Misc. bond : bond 0.00462 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 113 time to evaluate : 0.403 Fit side-chains REVERT: A 129 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 144 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6291 (mttm) REVERT: A 274 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: A 392 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8237 (mtmm) REVERT: A 441 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: A 451 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8000 (ttpp) REVERT: A 479 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7389 (ttt180) REVERT: A 507 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6198 (mp10) REVERT: A 528 SER cc_start: 0.8859 (t) cc_final: 0.8499 (p) REVERT: A 549 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: A 596 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 625 PHE cc_start: 0.7462 (m-10) cc_final: 0.6379 (t80) REVERT: A 660 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 688 TYR cc_start: 0.7840 (m-80) cc_final: 0.7448 (m-80) REVERT: A 793 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: A 808 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: A 985 GLN cc_start: 0.8773 (tp40) cc_final: 0.7715 (mp10) REVERT: A 1073 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: A 1253 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8199 (tm) REVERT: A 1296 ILE cc_start: 0.3552 (OUTLIER) cc_final: 0.3216 (mp) REVERT: A 1363 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7848 (p) outliers start: 53 outliers final: 29 residues processed: 153 average time/residue: 0.4558 time to fit residues: 76.4227 Evaluate side-chains 155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115439 restraints weight = 13391.469| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.79 r_work: 0.3130 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11701 Z= 0.143 Angle : 0.569 11.402 15930 Z= 0.280 Chirality : 0.042 0.271 1753 Planarity : 0.004 0.040 1969 Dihedral : 9.815 179.151 2118 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.93 % Allowed : 22.14 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1378 helix: 1.81 (0.19), residues: 782 sheet: -1.35 (0.59), residues: 78 loop : -1.15 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 729 TYR 0.015 0.001 TYR A1129 PHE 0.023 0.001 PHE A1203 TRP 0.038 0.001 TRP A 687 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11697) covalent geometry : angle 0.56936 / 0.28 (15924) SS BOND : bond 0.00174 / 0.09 ( 3) SS BOND : angle 0.63645 / 0.28 ( 6) hydrogen bonds : bond 0.04399 / 2.86 ( 603) hydrogen bonds : angle 4.20186 / 2.98 ( 1749) Misc. bond : bond 0.00431 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.289 Fit side-chains REVERT: A 129 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 274 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 392 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8237 (mtmm) REVERT: A 441 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: A 451 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7976 (ttpp) REVERT: A 479 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7383 (ttt180) REVERT: A 507 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: A 528 SER cc_start: 0.8765 (t) cc_final: 0.8432 (p) REVERT: A 549 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7977 (mtt) REVERT: A 596 GLU cc_start: 0.8013 (tt0) cc_final: 0.7752 (mt-10) REVERT: A 660 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 793 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6553 (mm-30) REVERT: A 808 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6514 (mt-10) REVERT: A 985 GLN cc_start: 0.8752 (tp40) cc_final: 0.7692 (mp10) REVERT: A 1073 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: A 1253 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8189 (tm) REVERT: A 1296 ILE cc_start: 0.3513 (OUTLIER) cc_final: 0.3225 (mp) REVERT: A 1363 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7814 (p) outliers start: 47 outliers final: 27 residues processed: 152 average time/residue: 0.4412 time to fit residues: 73.5111 Evaluate side-chains 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 431 GLN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116262 restraints weight = 13514.782| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.77 r_work: 0.3142 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11701 Z= 0.131 Angle : 0.564 11.275 15930 Z= 0.277 Chirality : 0.042 0.264 1753 Planarity : 0.004 0.040 1969 Dihedral : 9.618 179.858 2115 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.51 % Allowed : 22.64 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.23), residues: 1378 helix: 1.87 (0.19), residues: 781 sheet: -1.33 (0.59), residues: 78 loop : -1.12 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 729 TYR 0.014 0.001 TYR A1129 PHE 0.027 0.001 PHE A 774 TRP 0.045 0.001 TRP A 687 HIS 0.002 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11697) covalent geometry : angle 0.56382 / 0.28 (15924) SS BOND : bond 0.00149 / 0.07 ( 3) SS BOND : angle 0.58323 / 0.25 ( 6) hydrogen bonds : bond 0.04247 / 2.76 ( 603) hydrogen bonds : angle 4.17367 / 2.97 ( 1749) Misc. bond : bond 0.00418 / 0.22 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.339 Fit side-chains REVERT: A 129 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 144 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.5879 (mttm) REVERT: A 274 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 392 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8249 (mtmm) REVERT: A 441 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7765 (mtp180) REVERT: A 451 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8001 (ttpp) REVERT: A 479 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7390 (ttt180) REVERT: A 507 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6393 (mp10) REVERT: A 528 SER cc_start: 0.8755 (t) cc_final: 0.8439 (p) REVERT: A 596 GLU cc_start: 0.7965 (tt0) cc_final: 0.7703 (mt-10) REVERT: A 660 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8145 (p) REVERT: A 793 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: A 804 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6524 (ttp-170) REVERT: A 985 GLN cc_start: 0.8739 (tp40) cc_final: 0.7693 (mp10) REVERT: A 1073 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: A 1113 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (ptm) REVERT: A 1253 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8203 (tm) REVERT: A 1296 ILE cc_start: 0.3425 (OUTLIER) cc_final: 0.3174 (mp) REVERT: A 1363 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7748 (p) outliers start: 42 outliers final: 22 residues processed: 144 average time/residue: 0.4129 time to fit residues: 64.8871 Evaluate side-chains 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1056 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 420 GLN A 608 ASN A1242 GLN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116981 restraints weight = 13609.184| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.81 r_work: 0.3158 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11701 Z= 0.128 Angle : 0.547 11.120 15930 Z= 0.269 Chirality : 0.041 0.250 1753 Planarity : 0.004 0.040 1969 Dihedral : 9.465 179.557 2115 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.26 % Allowed : 22.97 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1378 helix: 1.91 (0.19), residues: 782 sheet: -1.43 (0.53), residues: 91 loop : -1.01 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 729 TYR 0.013 0.001 TYR A1129 PHE 0.023 0.001 PHE A 774 TRP 0.042 0.001 TRP A 687 HIS 0.002 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11697) covalent geometry : angle 0.54745 / 0.27 (15924) SS BOND : bond 0.00154 / 0.08 ( 3) SS BOND : angle 0.51829 / 0.22 ( 6) hydrogen bonds : bond 0.04123 / 2.68 ( 603) hydrogen bonds : angle 4.13203 / 2.94 ( 1749) Misc. bond : bond 0.00413 / 0.22 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.54 seconds wall clock time: 54 minutes 27.71 seconds (3267.71 seconds total)