Starting phenix.real_space_refine on Sun Jun 8 16:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.map" model { file = "/net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wi0_37554/06_2025/8wi0_37554.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 59 5.16 5 C 6233 2.51 5 N 1657 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 9580 Classifications: {'peptide': 1220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 1182} Chain breaks: 2 Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 136 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 5.79, per 1000 atoms: 0.60 Number of scatterers: 9716 At special positions: 0 Unit cell: (75.04, 112.56, 154.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 1 15.00 O 1766 8.00 N 1657 7.00 C 6233 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 70.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 140 Processing helix chain 'A' and resid 141 through 161 removed outlier: 3.539A pdb=" N ASN A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 209 removed outlier: 5.427A pdb=" N THR A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 214 through 263 removed outlier: 3.539A pdb=" N SER A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.556A pdb=" N CYS A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.412A pdb=" N VAL A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 364 removed outlier: 3.991A pdb=" N GLY A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.623A pdb=" N LYS A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 373 through 402 removed outlier: 3.753A pdb=" N PHE A 377 " --> pdb=" O TRP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 424 removed outlier: 4.382A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 472 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 686 through 702 Processing helix chain 'A' and resid 716 through 728 Processing helix chain 'A' and resid 730 through 735 removed outlier: 4.138A pdb=" N LYS A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 734 " --> pdb=" O HIS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 750 removed outlier: 3.810A pdb=" N TYR A 746 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 748 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 749 " --> pdb=" O TYR A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 842 through 854 removed outlier: 4.028A pdb=" N TYR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 887 removed outlier: 3.842A pdb=" N GLY A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 956 Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.961A pdb=" N PHE A 963 " --> pdb=" O PRO A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1011 removed outlier: 3.750A pdb=" N ILE A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 978 " --> pdb=" O ARG A 974 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A 979 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) Proline residue: A 987 - end of helix Processing helix chain 'A' and resid 1011 through 1046 removed outlier: 3.974A pdb=" N LEU A1015 " --> pdb=" O PHE A1011 " (cutoff:3.500A) Proline residue: A1020 - end of helix removed outlier: 3.529A pdb=" N ILE A1036 " --> pdb=" O SER A1032 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.935A pdb=" N PHE A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1067 Processing helix chain 'A' and resid 1071 through 1120 Proline residue: A1087 - end of helix Processing helix chain 'A' and resid 1125 through 1139 Processing helix chain 'A' and resid 1141 through 1170 removed outlier: 4.215A pdb=" N PHE A1145 " --> pdb=" O GLY A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1234 No H-bonds generated for 'chain 'A' and resid 1232 through 1234' Processing helix chain 'A' and resid 1235 through 1241 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1262 through 1268 Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1295 through 1306 Processing helix chain 'A' and resid 1308 through 1314 Processing helix chain 'A' and resid 1324 through 1328 Processing helix chain 'A' and resid 1331 through 1345 Processing helix chain 'A' and resid 1361 through 1376 Processing helix chain 'A' and resid 1387 through 1392 removed outlier: 3.601A pdb=" N VAL A1391 " --> pdb=" O ARG A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1416 removed outlier: 3.536A pdb=" N SER A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1435 Processing helix chain 'B' and resid 48 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.804A pdb=" N ILE A 490 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 618 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 575 through 576 removed outlier: 4.026A pdb=" N ALA A 498 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A 613 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 625 through 628 removed outlier: 3.558A pdb=" N ILE A 707 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 709 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 706 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A 740 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 708 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 591 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A 592 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET A 756 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS A 594 " --> pdb=" O MET A 756 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 753 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG A 764 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 755 " --> pdb=" O THR A 762 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 762 " --> pdb=" O PHE A 755 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 894 Processing sheet with id=AA5, first strand: chain 'A' and resid 1210 through 1213 removed outlier: 5.951A pdb=" N LYS A1211 " --> pdb=" O MET A1200 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N MET A1200 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1213 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1210 through 1213 removed outlier: 5.951A pdb=" N LYS A1211 " --> pdb=" O MET A1200 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N MET A1200 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1213 " --> pdb=" O ALA A1198 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A1196 " --> pdb=" O CYS A1250 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A1250 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A1198 " --> pdb=" O GLY A1248 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A1248 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1273 removed outlier: 3.751A pdb=" N SER A1271 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A1351 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A1384 " --> pdb=" O LEU A1351 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A1353 " --> pdb=" O ILE A1384 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A1396 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A1224 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1400 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A1409 " --> pdb=" O ILE A1397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1399 " --> pdb=" O GLU A1407 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A1407 " --> pdb=" O VAL A1399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1282 through 1283 646 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1901 1.33 - 1.45: 2289 1.45 - 1.57: 5609 1.57 - 1.69: 2 1.69 - 1.81: 99 Bond restraints: 9900 Sorted by residual: bond pdb=" O3P SEP B 60 " pdb=" P SEP B 60 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O1P SEP B 60 " pdb=" P SEP B 60 " ideal model delta sigma weight residual 1.610 1.512 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O2P SEP B 60 " pdb=" P SEP B 60 " ideal model delta sigma weight residual 1.610 1.518 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CB PRO A 162 " pdb=" CG PRO A 162 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.17e+00 bond pdb=" CA THR A 450 " pdb=" C THR A 450 " ideal model delta sigma weight residual 1.520 1.544 -0.024 1.23e-02 6.61e+03 3.65e+00 ... (remaining 9895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 13043 1.73 - 3.47: 303 3.47 - 5.20: 46 5.20 - 6.93: 7 6.93 - 8.66: 2 Bond angle restraints: 13401 Sorted by residual: angle pdb=" N ILE A 643 " pdb=" CA ILE A 643 " pdb=" C ILE A 643 " ideal model delta sigma weight residual 112.96 107.59 5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" N THR A 450 " pdb=" CA THR A 450 " pdb=" C THR A 450 " ideal model delta sigma weight residual 112.75 119.82 -7.07 1.36e+00 5.41e-01 2.70e+01 angle pdb=" N GLY A1009 " pdb=" CA GLY A1009 " pdb=" C GLY A1009 " ideal model delta sigma weight residual 114.16 109.74 4.42 1.21e+00 6.83e-01 1.33e+01 angle pdb=" N LEU A 273 " pdb=" CA LEU A 273 " pdb=" C LEU A 273 " ideal model delta sigma weight residual 113.12 108.90 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" N GLY A 319 " pdb=" CA GLY A 319 " pdb=" C GLY A 319 " ideal model delta sigma weight residual 114.66 110.94 3.72 1.24e+00 6.50e-01 8.99e+00 ... (remaining 13396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 5065 16.42 - 32.85: 653 32.85 - 49.27: 180 49.27 - 65.69: 40 65.69 - 82.11: 14 Dihedral angle restraints: 5952 sinusoidal: 2355 harmonic: 3597 Sorted by residual: dihedral pdb=" CA PHE A 625 " pdb=" C PHE A 625 " pdb=" N ALA A 626 " pdb=" CA ALA A 626 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY A 404 " pdb=" C GLY A 404 " pdb=" N VAL A 405 " pdb=" CA VAL A 405 " ideal model delta harmonic sigma weight residual -180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A1354 " pdb=" C ASP A1354 " pdb=" N GLU A1355 " pdb=" CA GLU A1355 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1059 0.035 - 0.070: 378 0.070 - 0.104: 93 0.104 - 0.139: 36 0.139 - 0.174: 4 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB THR A 402 " pdb=" CA THR A 402 " pdb=" OG1 THR A 402 " pdb=" CG2 THR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA THR A 450 " pdb=" N THR A 450 " pdb=" C THR A 450 " pdb=" CB THR A 450 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ASN A 642 " pdb=" N ASN A 642 " pdb=" C ASN A 642 " pdb=" CB ASN A 642 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1567 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 57 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C GLU B 57 " -0.083 2.00e-02 2.50e+03 pdb=" O GLU B 57 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY B 58 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 330 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 331 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 855 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 856 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.035 5.00e-02 4.00e+02 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 287 2.71 - 3.26: 9806 3.26 - 3.80: 15853 3.80 - 4.35: 19820 4.35 - 4.90: 33612 Nonbonded interactions: 79378 Sorted by model distance: nonbonded pdb=" OG SER A 337 " pdb=" OD2 ASP B 48 " model vdw 2.162 3.040 nonbonded pdb=" O ALA A1155 " pdb=" OG1 THR A1158 " model vdw 2.228 3.040 nonbonded pdb=" O LEU A 128 " pdb=" NH2 ARG A1041 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR A 496 " pdb=" OE1 GLU A 616 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASN A 996 " pdb=" OG1 THR A1146 " model vdw 2.266 3.040 ... (remaining 79373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 9900 Z= 0.183 Angle : 0.639 8.664 13401 Z= 0.391 Chirality : 0.040 0.174 1570 Planarity : 0.005 0.071 1680 Dihedral : 16.326 82.114 3620 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 0.28 % Allowed : 17.42 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1228 helix: 1.54 (0.18), residues: 805 sheet: 0.13 (0.74), residues: 52 loop : -1.21 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.004 0.001 HIS A1029 PHE 0.012 0.001 PHE A 398 TYR 0.013 0.001 TYR A 330 ARG 0.010 0.000 ARG A 957 Details of bonding type rmsd hydrogen bonds : bond 0.15835 ( 645) hydrogen bonds : angle 5.72931 ( 1896) covalent geometry : bond 0.00350 ( 9900) covalent geometry : angle 0.63921 (13401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 1.1364 time to fit residues: 131.4971 Evaluate side-chains 95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN A1275 GLN A1417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.197409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147761 restraints weight = 10253.824| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.26 r_work: 0.3342 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9900 Z= 0.164 Angle : 0.550 8.221 13401 Z= 0.300 Chirality : 0.041 0.162 1570 Planarity : 0.005 0.065 1680 Dihedral : 5.049 61.228 1341 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 2.45 % Allowed : 18.08 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1228 helix: 1.52 (0.18), residues: 795 sheet: 0.87 (0.73), residues: 51 loop : -1.33 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1097 HIS 0.004 0.001 HIS A1029 PHE 0.018 0.002 PHE A 434 TYR 0.013 0.001 TYR A 330 ARG 0.004 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.06995 ( 645) hydrogen bonds : angle 4.80480 ( 1896) covalent geometry : bond 0.00346 ( 9900) covalent geometry : angle 0.55031 (13401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 177 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 334 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: A 338 ARG cc_start: 0.7981 (mpt90) cc_final: 0.7753 (mpt180) REVERT: A 492 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6760 (mpt) REVERT: A 1238 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7859 (ttm) outliers start: 26 outliers final: 12 residues processed: 120 average time/residue: 1.6019 time to fit residues: 208.8410 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain B residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A1085 GLN A1431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.196113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147447 restraints weight = 10320.986| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.42 r_work: 0.3239 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9900 Z= 0.151 Angle : 0.524 9.118 13401 Z= 0.282 Chirality : 0.041 0.224 1570 Planarity : 0.005 0.063 1680 Dihedral : 4.783 64.884 1339 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.30 % Allowed : 18.55 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1228 helix: 1.66 (0.18), residues: 797 sheet: 0.99 (0.73), residues: 51 loop : -1.15 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1097 HIS 0.003 0.001 HIS A1029 PHE 0.016 0.001 PHE A 434 TYR 0.011 0.001 TYR A 330 ARG 0.003 0.000 ARG A 946 Details of bonding type rmsd hydrogen bonds : bond 0.06727 ( 645) hydrogen bonds : angle 4.59891 ( 1896) covalent geometry : bond 0.00311 ( 9900) covalent geometry : angle 0.52351 (13401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 334 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7627 (mtm) REVERT: A 338 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7660 (mpt180) REVERT: A 631 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: A 953 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7784 (ttp80) REVERT: A 1095 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: A 1354 ASP cc_start: 0.7407 (t0) cc_final: 0.7203 (t70) REVERT: B 59 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7656 (mp) outliers start: 35 outliers final: 15 residues processed: 140 average time/residue: 1.0611 time to fit residues: 161.3259 Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.189397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125328 restraints weight = 10377.819| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.84 r_work: 0.3210 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9900 Z= 0.175 Angle : 0.550 7.460 13401 Z= 0.297 Chirality : 0.042 0.303 1570 Planarity : 0.005 0.063 1680 Dihedral : 4.801 65.665 1339 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.05 % Allowed : 18.46 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1228 helix: 1.65 (0.18), residues: 796 sheet: 1.15 (0.74), residues: 51 loop : -1.17 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1097 HIS 0.004 0.001 HIS A 421 PHE 0.020 0.002 PHE A 434 TYR 0.011 0.001 TYR A1135 ARG 0.003 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.07220 ( 645) hydrogen bonds : angle 4.65493 ( 1896) covalent geometry : bond 0.00388 ( 9900) covalent geometry : angle 0.55028 (13401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8754 (ptp) REVERT: A 334 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7519 (mtm) REVERT: A 631 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: A 953 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7306 (ttp80) REVERT: A 957 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6767 (ttp-110) REVERT: A 1040 LYS cc_start: 0.8038 (tttm) cc_final: 0.7746 (tttp) REVERT: A 1095 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7723 (mpp) REVERT: A 1221 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 1238 MET cc_start: 0.7979 (tpp) cc_final: 0.7704 (ttm) REVERT: B 59 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7685 (mp) outliers start: 43 outliers final: 19 residues processed: 144 average time/residue: 1.0191 time to fit residues: 159.7815 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.194146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150237 restraints weight = 10315.821| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.35 r_work: 0.3262 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9900 Z= 0.148 Angle : 0.515 7.687 13401 Z= 0.277 Chirality : 0.040 0.151 1570 Planarity : 0.004 0.062 1680 Dihedral : 4.493 69.670 1337 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.39 % Allowed : 19.49 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1228 helix: 1.78 (0.18), residues: 798 sheet: 1.14 (0.74), residues: 51 loop : -1.14 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1097 HIS 0.003 0.001 HIS A 421 PHE 0.015 0.001 PHE A 434 TYR 0.011 0.001 TYR A1135 ARG 0.002 0.000 ARG A 946 Details of bonding type rmsd hydrogen bonds : bond 0.06656 ( 645) hydrogen bonds : angle 4.51953 ( 1896) covalent geometry : bond 0.00304 ( 9900) covalent geometry : angle 0.51480 (13401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7882 (pttm) REVERT: A 351 THR cc_start: 0.8566 (m) cc_final: 0.8353 (p) REVERT: A 492 MET cc_start: 0.8163 (mpp) cc_final: 0.7961 (mtt) REVERT: A 589 LYS cc_start: 0.7364 (mtpt) cc_final: 0.7078 (mmtm) REVERT: A 631 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: A 953 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7980 (ttp80) REVERT: A 1095 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7841 (mpp) REVERT: A 1166 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6450 (t80) REVERT: A 1238 MET cc_start: 0.8248 (tpp) cc_final: 0.7969 (ttm) REVERT: B 59 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8040 (mp) outliers start: 36 outliers final: 19 residues processed: 144 average time/residue: 1.1034 time to fit residues: 172.7739 Evaluate side-chains 135 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.184086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118670 restraints weight = 10366.068| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3154 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9900 Z= 0.202 Angle : 0.577 8.467 13401 Z= 0.309 Chirality : 0.043 0.239 1570 Planarity : 0.005 0.064 1680 Dihedral : 4.679 79.112 1337 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.86 % Allowed : 19.40 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1228 helix: 1.63 (0.18), residues: 797 sheet: 0.93 (0.73), residues: 51 loop : -1.16 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1097 HIS 0.004 0.001 HIS A 139 PHE 0.023 0.002 PHE A 434 TYR 0.013 0.001 TYR A1135 ARG 0.003 0.000 ARG A1096 Details of bonding type rmsd hydrogen bonds : bond 0.07796 ( 645) hydrogen bonds : angle 4.67833 ( 1896) covalent geometry : bond 0.00457 ( 9900) covalent geometry : angle 0.57676 (13401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7922 (pttm) REVERT: A 589 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7044 (mmtm) REVERT: A 631 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: A 953 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7491 (ttp80) REVERT: A 1116 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8072 (mmt) REVERT: A 1238 MET cc_start: 0.7906 (tpp) cc_final: 0.7557 (ttm) REVERT: A 1381 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.4211 (tmm) REVERT: B 57 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: B 59 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7658 (mp) outliers start: 41 outliers final: 21 residues processed: 149 average time/residue: 1.0675 time to fit residues: 173.2576 Evaluate side-chains 138 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.192937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151289 restraints weight = 10395.315| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.09 r_work: 0.3262 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9900 Z= 0.147 Angle : 0.524 8.632 13401 Z= 0.279 Chirality : 0.040 0.242 1570 Planarity : 0.004 0.060 1680 Dihedral : 4.603 82.167 1337 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.20 % Allowed : 20.24 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1228 helix: 1.78 (0.18), residues: 797 sheet: 1.02 (0.73), residues: 51 loop : -1.12 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.003 0.001 HIS A 421 PHE 0.014 0.001 PHE A 434 TYR 0.013 0.001 TYR A1135 ARG 0.002 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.06749 ( 645) hydrogen bonds : angle 4.51088 ( 1896) covalent geometry : bond 0.00300 ( 9900) covalent geometry : angle 0.52391 (13401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7960 (pttm) REVERT: A 360 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 491 GLU cc_start: 0.7682 (tt0) cc_final: 0.7004 (pp20) REVERT: A 586 GLN cc_start: 0.7851 (mt0) cc_final: 0.7125 (tt0) REVERT: A 631 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: A 1095 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7873 (mpp) REVERT: A 1166 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 1238 MET cc_start: 0.8444 (tpp) cc_final: 0.8186 (ttm) outliers start: 34 outliers final: 17 residues processed: 142 average time/residue: 1.3048 time to fit residues: 200.5723 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.188770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.157905 restraints weight = 10417.081| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.51 r_work: 0.3155 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9900 Z= 0.207 Angle : 0.591 9.105 13401 Z= 0.315 Chirality : 0.044 0.251 1570 Planarity : 0.005 0.066 1680 Dihedral : 4.697 79.983 1337 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.30 % Allowed : 20.90 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1228 helix: 1.66 (0.18), residues: 791 sheet: 0.95 (0.75), residues: 51 loop : -1.05 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1097 HIS 0.005 0.001 HIS A 139 PHE 0.027 0.002 PHE A 434 TYR 0.013 0.001 TYR A1135 ARG 0.005 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.07873 ( 645) hydrogen bonds : angle 4.66868 ( 1896) covalent geometry : bond 0.00472 ( 9900) covalent geometry : angle 0.59147 (13401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8006 (pttm) REVERT: A 401 ILE cc_start: 0.7607 (mt) cc_final: 0.7355 (mm) REVERT: A 491 GLU cc_start: 0.7642 (tt0) cc_final: 0.6623 (pp20) REVERT: A 493 LYS cc_start: 0.8529 (mptm) cc_final: 0.8302 (mptp) REVERT: A 631 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: A 641 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: A 1095 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: A 1238 MET cc_start: 0.8179 (tpp) cc_final: 0.7842 (ttm) outliers start: 35 outliers final: 22 residues processed: 139 average time/residue: 1.3889 time to fit residues: 210.4003 Evaluate side-chains 137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.186151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122530 restraints weight = 10434.093| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.65 r_work: 0.3208 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9900 Z= 0.149 Angle : 0.535 8.624 13401 Z= 0.286 Chirality : 0.041 0.186 1570 Planarity : 0.004 0.060 1680 Dihedral : 4.612 81.211 1337 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.26 % Allowed : 21.85 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1228 helix: 1.88 (0.18), residues: 784 sheet: 1.08 (0.75), residues: 51 loop : -0.93 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.004 0.001 HIS A 487 PHE 0.013 0.001 PHE A1091 TYR 0.012 0.001 TYR A1135 ARG 0.004 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.06653 ( 645) hydrogen bonds : angle 4.49012 ( 1896) covalent geometry : bond 0.00306 ( 9900) covalent geometry : angle 0.53500 (13401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.065 Fit side-chains REVERT: A 138 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7965 (pttm) REVERT: A 360 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 438 THR cc_start: 0.9028 (m) cc_final: 0.8364 (p) REVERT: A 491 GLU cc_start: 0.7638 (tt0) cc_final: 0.7225 (tt0) REVERT: A 493 LYS cc_start: 0.8449 (mptm) cc_final: 0.8049 (mptm) REVERT: A 586 GLN cc_start: 0.7926 (mt0) cc_final: 0.6898 (tt0) REVERT: A 630 GLN cc_start: 0.7446 (mt0) cc_final: 0.6782 (pm20) REVERT: A 641 ASP cc_start: 0.7556 (m-30) cc_final: 0.7277 (m-30) REVERT: A 710 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6637 (p0) REVERT: A 1238 MET cc_start: 0.7972 (tpp) cc_final: 0.7647 (ttm) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 1.1369 time to fit residues: 166.0830 Evaluate side-chains 131 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.184990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120744 restraints weight = 10458.035| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.69 r_work: 0.3275 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9900 Z= 0.163 Angle : 0.548 9.639 13401 Z= 0.292 Chirality : 0.041 0.165 1570 Planarity : 0.004 0.060 1680 Dihedral : 4.588 79.604 1337 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 22.22 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1228 helix: 1.87 (0.18), residues: 784 sheet: 0.94 (0.73), residues: 51 loop : -0.87 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1097 HIS 0.005 0.001 HIS A 421 PHE 0.018 0.002 PHE A 434 TYR 0.014 0.001 TYR A1135 ARG 0.004 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.06966 ( 645) hydrogen bonds : angle 4.52973 ( 1896) covalent geometry : bond 0.00351 ( 9900) covalent geometry : angle 0.54778 (13401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.864 Fit side-chains REVERT: A 138 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8026 (pttm) REVERT: A 360 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 438 THR cc_start: 0.9126 (m) cc_final: 0.8553 (p) REVERT: A 491 GLU cc_start: 0.7683 (tt0) cc_final: 0.7272 (tt0) REVERT: A 493 LYS cc_start: 0.8518 (mptm) cc_final: 0.8061 (mptm) REVERT: A 630 GLN cc_start: 0.7407 (mt0) cc_final: 0.6751 (pm20) REVERT: A 641 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: A 710 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6557 (p0) REVERT: A 1238 MET cc_start: 0.8284 (tpp) cc_final: 0.7965 (ttm) outliers start: 22 outliers final: 15 residues processed: 133 average time/residue: 1.2209 time to fit residues: 178.5595 Evaluate side-chains 130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.190892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149726 restraints weight = 10338.210| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.13 r_work: 0.3153 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9900 Z= 0.152 Angle : 0.547 9.374 13401 Z= 0.290 Chirality : 0.041 0.175 1570 Planarity : 0.004 0.059 1680 Dihedral : 4.578 79.604 1337 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 22.60 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1228 helix: 1.92 (0.18), residues: 784 sheet: 1.01 (0.73), residues: 51 loop : -0.90 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1097 HIS 0.005 0.001 HIS A 487 PHE 0.015 0.001 PHE A 434 TYR 0.013 0.001 TYR A1135 ARG 0.004 0.000 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.06689 ( 645) hydrogen bonds : angle 4.48511 ( 1896) covalent geometry : bond 0.00321 ( 9900) covalent geometry : angle 0.54704 (13401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8039.64 seconds wall clock time: 142 minutes 17.39 seconds (8537.39 seconds total)