Starting phenix.real_space_refine on Thu Mar 13 15:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.map" model { file = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7op3_13012/03_2025/7op3_13012.cif" } resolution = 3.5 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= -0.000 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5709 2.51 5 N 1460 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8758 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.68 Number of scatterers: 8772 At special positions: 0 Unit cell: (90.688, 92.352, 132.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1549 8.00 N 1460 7.00 C 5709 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: 2.48 Conformation dependent library (CDL) restraints added in 852.7 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 46.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.233A pdb=" N TYR A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.633A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.612A pdb=" N VAL A 401 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 446 removed outlier: 3.632A pdb=" N SER A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.644A pdb=" N ASP A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 534 " --> pdb=" O HIS A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 534' Processing helix chain 'A' and resid 571 through 577 removed outlier: 3.903A pdb=" N SER A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 618 removed outlier: 4.166A pdb=" N PHE A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 616 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 617 " --> pdb=" O ASN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.717A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 665 through 671 removed outlier: 4.276A pdb=" N ASN A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 748 through 757 Processing helix chain 'A' and resid 773 through 782 removed outlier: 3.979A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 882 through 891 Processing helix chain 'A' and resid 904 through 908 removed outlier: 3.741A pdb=" N ASN A 907 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 908 " --> pdb=" O LYS A 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 904 through 908' Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.591A pdb=" N VAL A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 921 " --> pdb=" O ASP A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 960 through 972 removed outlier: 3.599A pdb=" N SER A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1052 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1072 through 1086 Processing helix chain 'A' and resid 1099 through 1106 removed outlier: 3.568A pdb=" N LEU A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1167 removed outlier: 3.744A pdb=" N GLU A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1172 Processing helix chain 'A' and resid 1176 through 1187 removed outlier: 3.736A pdb=" N LEU A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1196 Processing helix chain 'A' and resid 1215 through 1242 removed outlier: 3.635A pdb=" N VAL A1220 " --> pdb=" O ARG A1216 " (cutoff:3.500A) Proline residue: A1221 - end of helix removed outlier: 3.550A pdb=" N GLN A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1281 removed outlier: 3.549A pdb=" N THR A1264 " --> pdb=" O ASN A1260 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A1265 " --> pdb=" O SER A1261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1266 " --> pdb=" O GLU A1262 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A1277 " --> pdb=" O GLU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1314 removed outlier: 4.204A pdb=" N LEU A1298 " --> pdb=" O THR A1294 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A1308 " --> pdb=" O THR A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1324 removed outlier: 4.002A pdb=" N GLU A1321 " --> pdb=" O TYR A1317 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A1322 " --> pdb=" O TRP A1318 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A1323 " --> pdb=" O LEU A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1354 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1377 through 1389 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.723A pdb=" N MET A 209 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 218 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 274 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 221 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 272 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 290 removed outlier: 4.188A pdb=" N SER A 322 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 288 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 320 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR A 290 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG A 318 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 321 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 338 " --> pdb=" O HIS A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 6.884A pdb=" N VAL A 559 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 510 removed outlier: 6.735A pdb=" N VAL A 506 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 496 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 508 " --> pdb=" O CYS A 494 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 494 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE A 495 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 660 through 662 removed outlier: 6.401A pdb=" N GLY A1109 " --> pdb=" O PHE A1123 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A1125 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER A1111 " --> pdb=" O SER A1125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 676 through 677 Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 697 removed outlier: 7.450A pdb=" N ILE A 930 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A 695 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 928 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL A 697 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 926 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 924 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 930 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 894 " --> pdb=" O ILE A 930 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 955 through 956 removed outlier: 6.582A pdb=" N MET A 955 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE A1039 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A1068 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A1041 " --> pdb=" O TYR A1068 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 984 353 hydrogen bonds defined for protein. 1035 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: 3.14 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2104 1.46 - 1.58: 4078 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 8990 Sorted by residual: bond pdb=" C TRP A1295 " pdb=" N PRO A1296 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" CB ARG A1366 " pdb=" CG ARG A1366 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB TYR A1037 " pdb=" CG TYR A1037 " ideal model delta sigma weight residual 1.512 1.542 -0.030 2.20e-02 2.07e+03 1.84e+00 bond pdb=" C ARG A1285 " pdb=" N PRO A1286 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.72e+00 bond pdb=" CA THR A 394 " pdb=" CB THR A 394 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.53e-02 4.27e+03 1.69e+00 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11734 1.75 - 3.50: 373 3.50 - 5.25: 64 5.25 - 7.00: 27 7.00 - 8.75: 9 Bond angle restraints: 12207 Sorted by residual: angle pdb=" CA THR A 394 " pdb=" CB THR A 394 " pdb=" CG2 THR A 394 " ideal model delta sigma weight residual 110.50 117.05 -6.55 1.70e+00 3.46e-01 1.48e+01 angle pdb=" N TYR A1037 " pdb=" CA TYR A1037 " pdb=" C TYR A1037 " ideal model delta sigma weight residual 111.36 115.40 -4.04 1.09e+00 8.42e-01 1.37e+01 angle pdb=" C PHE A 782 " pdb=" N THR A 783 " pdb=" CA THR A 783 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N TRP A 350 " pdb=" CA TRP A 350 " pdb=" CB TRP A 350 " ideal model delta sigma weight residual 110.16 115.16 -5.00 1.48e+00 4.57e-01 1.14e+01 angle pdb=" N ARG A 292 " pdb=" CA ARG A 292 " pdb=" C ARG A 292 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 ... (remaining 12202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4768 17.62 - 35.23: 463 35.23 - 52.85: 87 52.85 - 70.47: 14 70.47 - 88.08: 8 Dihedral angle restraints: 5340 sinusoidal: 2123 harmonic: 3217 Sorted by residual: dihedral pdb=" CA VAL A 453 " pdb=" C VAL A 453 " pdb=" N PHE A 454 " pdb=" CA PHE A 454 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG A1285 " pdb=" C ARG A1285 " pdb=" N PRO A1286 " pdb=" CA PRO A1286 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU A1293 " pdb=" CG GLU A1293 " pdb=" CD GLU A1293 " pdb=" OE1 GLU A1293 " ideal model delta sinusoidal sigma weight residual 0.00 88.08 -88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1170 0.068 - 0.135: 200 0.135 - 0.203: 15 0.203 - 0.270: 3 0.270 - 0.338: 3 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CB ILE A 660 " pdb=" CA ILE A 660 " pdb=" CG1 ILE A 660 " pdb=" CG2 ILE A 660 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB THR A 263 " pdb=" CA THR A 263 " pdb=" OG1 THR A 263 " pdb=" CG2 THR A 263 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1388 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 350 " 0.028 2.00e-02 2.50e+03 3.46e-02 2.98e+01 pdb=" CG TRP A 350 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP A 350 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 350 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 350 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 350 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 350 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1037 " 0.028 2.00e-02 2.50e+03 1.97e-02 7.79e+00 pdb=" CG TYR A1037 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A1037 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A1037 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A1037 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A1037 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1037 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1037 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 868 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 869 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 869 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 869 " 0.034 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2235 2.80 - 3.33: 8195 3.33 - 3.85: 14383 3.85 - 4.38: 15972 4.38 - 4.90: 27952 Nonbonded interactions: 68737 Sorted by model distance: nonbonded pdb=" OD1 ASN A 669 " pdb=" OG SER A1143 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 331 " pdb=" O VAL A 371 " model vdw 2.293 3.040 nonbonded pdb=" OG SER A1001 " pdb=" O ASN A1003 " model vdw 2.293 3.040 nonbonded pdb=" O LYS A 673 " pdb=" OG SER A1089 " model vdw 2.313 3.040 nonbonded pdb=" O SER A 949 " pdb=" OG SER A 949 " model vdw 2.315 3.040 ... (remaining 68732 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.260 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 0.042 8990 Z= 0.235 Angle : 0.776 8.749 12207 Z= 0.398 Chirality : 0.052 0.338 1391 Planarity : 0.006 0.061 1523 Dihedral : 14.575 88.082 3258 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.24 (0.24), residues: 1088 helix: 0.28 (0.24), residues: 437 sheet: -0.72 (0.52), residues: 101 loop : -1.80 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP A 350 HIS 0.004 0.001 HIS A1052 PHE 0.042 0.002 PHE A 780 TYR 0.042 0.002 TYR A1037 ARG 0.012 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.952 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1829 time to fit residues: 28.1908 Evaluate side-chains 82 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1242 GLN ** A1257 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 = 0.4229 r_free = 0.4229 target = 0.197787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129019 restraints weight = 10431.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131403 restraints weight = 5988.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132557 restraints weight = 4408.042| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8990 Z= 0.233 Angle : 0.566 8.209 12207 Z= 0.289 Chirality : 0.043 0.166 1391 Planarity : 0.004 0.050 1523 Dihedral : 4.883 53.504 1210 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.73 % Allowed : 9.85 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.91 (0.25), residues: 1088 helix: 0.65 (0.24), residues: 457 sheet: -0.80 (0.51), residues: 104 loop : -1.74 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 350 HIS 0.004 0.001 HIS A 977 PHE 0.020 0.001 PHE A 536 TYR 0.015 0.002 TYR A1343 ARG 0.005 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.872 Fit side-chains REVERT: A 438 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7843 (ttm-80) REVERT: A 945 GLU cc_start: 0.8022 (tt0) cc_final: 0.7793 (tt0) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.1823 time to fit residues: 27.5213 Evaluate side-chains 94 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 1387 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.193408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120185 restraints weight = 10725.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123648 restraints weight = 6114.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125775 restraints weight = 4467.429| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8990 Z= 0.319 Angle : 0.597 7.124 12207 Z= 0.304 Chirality : 0.045 0.188 1391 Planarity : 0.004 0.038 1523 Dihedral : 4.941 58.964 1210 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.87 % Allowed : 14.73 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.96 (0.26), residues: 1088 helix: 0.59 (0.24), residues: 460 sheet: -0.84 (0.47), residues: 123 loop : -1.77 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.005 0.001 HIS A 977 PHE 0.016 0.002 PHE A 780 TYR 0.016 0.002 TYR A1343 ARG 0.004 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.974 Fit side-chains REVERT: A 868 MET cc_start: 0.4777 (OUTLIER) cc_final: 0.4514 (mtm) REVERT: A 945 GLU cc_start: 0.8124 (tt0) cc_final: 0.7889 (tt0) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.1804 time to fit residues: 29.5061 Evaluate side-chains 102 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 0.0170 chunk 29 optimal weight: 50.0000 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 351 ASN ** A1257 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 = 0.4200 r_free = 0.4200 target = 0.194982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123580 restraints weight = 10573.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126717 restraints weight = 6432.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128549 restraints weight = 4806.390| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8990 Z= 0.188 Angle : 0.534 6.976 12207 Z= 0.271 Chirality : 0.042 0.206 1391 Planarity : 0.004 0.035 1523 Dihedral : 4.759 56.266 1210 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.59 % Allowed : 16.08 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.74 (0.26), residues: 1088 helix: 0.86 (0.25), residues: 458 sheet: -0.78 (0.47), residues: 123 loop : -1.72 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.004 0.001 HIS A 977 PHE 0.016 0.001 PHE A1361 TYR 0.016 0.001 TYR A 887 ARG 0.003 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.942 Fit side-chains REVERT: A 945 GLU cc_start: 0.8012 (tt0) cc_final: 0.7784 (tt0) REVERT: A 1187 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (mp) outliers start: 25 outliers final: 16 residues processed: 115 average time/residue: 0.1699 time to fit residues: 29.6041 Evaluate side-chains 103 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 887 TYR Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.192703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118985 restraints weight = 10533.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122697 restraints weight = 5927.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124877 restraints weight = 4267.457| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8990 Z= 0.307 Angle : 0.583 6.903 12207 Z= 0.296 Chirality : 0.044 0.183 1391 Planarity : 0.004 0.036 1523 Dihedral : 4.840 52.883 1210 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.59 % Allowed : 17.22 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.26), residues: 1088 helix: 0.70 (0.24), residues: 457 sheet: -0.68 (0.49), residues: 117 loop : -1.75 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS A 977 PHE 0.015 0.001 PHE A1361 TYR 0.018 0.002 TYR A 887 ARG 0.002 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.054 Fit side-chains REVERT: A 945 GLU cc_start: 0.8188 (tt0) cc_final: 0.7937 (tt0) REVERT: A 1187 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8563 (mp) outliers start: 25 outliers final: 20 residues processed: 114 average time/residue: 0.1742 time to fit residues: 30.3647 Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1387 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 23 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 92 optimal weight: 0.0270 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124175 restraints weight = 10421.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127875 restraints weight = 5773.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129921 restraints weight = 4074.342| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8990 Z= 0.151 Angle : 0.528 7.342 12207 Z= 0.266 Chirality : 0.042 0.176 1391 Planarity : 0.004 0.037 1523 Dihedral : 4.629 50.612 1210 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.07 % Allowed : 18.26 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.52 (0.26), residues: 1088 helix: 1.11 (0.25), residues: 452 sheet: -0.65 (0.48), residues: 123 loop : -1.64 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS A 977 PHE 0.017 0.001 PHE A 536 TYR 0.015 0.001 TYR A 887 ARG 0.003 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.008 Fit side-chains REVERT: A 945 GLU cc_start: 0.8092 (tt0) cc_final: 0.7860 (tt0) REVERT: A 1187 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (mp) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.1764 time to fit residues: 29.0830 Evaluate side-chains 100 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 31 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** 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 = 0.4212 r_free = 0.4212 target = 0.196711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125262 restraints weight = 10563.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128388 restraints weight = 6139.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130005 restraints weight = 4287.690| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8990 Z= 0.166 Angle : 0.529 7.506 12207 Z= 0.264 Chirality : 0.042 0.164 1391 Planarity : 0.004 0.035 1523 Dihedral : 4.542 49.050 1210 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.18 % Allowed : 18.88 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.26), residues: 1088 helix: 1.09 (0.25), residues: 461 sheet: -0.67 (0.48), residues: 125 loop : -1.72 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.004 0.000 HIS A 977 PHE 0.016 0.001 PHE A 536 TYR 0.017 0.001 TYR A 255 ARG 0.002 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.916 Fit side-chains REVERT: A 251 TYR cc_start: 0.7415 (m-10) cc_final: 0.7026 (m-10) REVERT: A 328 TYR cc_start: 0.7716 (m-80) cc_final: 0.7509 (m-80) REVERT: A 945 GLU cc_start: 0.8114 (tt0) cc_final: 0.7880 (tt0) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.1730 time to fit residues: 26.9897 Evaluate side-chains 101 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN ** A1257 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 = 0.4183 r_free = 0.4183 target = 0.193562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122819 restraints weight = 10644.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124945 restraints weight = 6556.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125379 restraints weight = 4828.446| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8990 Z= 0.270 Angle : 0.567 7.893 12207 Z= 0.285 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.035 1523 Dihedral : 4.664 50.249 1210 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.59 % Allowed : 17.95 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.68 (0.26), residues: 1088 helix: 0.88 (0.24), residues: 463 sheet: -0.56 (0.48), residues: 123 loop : -1.74 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1245 HIS 0.004 0.001 HIS A 977 PHE 0.016 0.001 PHE A 536 TYR 0.016 0.002 TYR A1343 ARG 0.002 0.000 ARG A1288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.059 Fit side-chains REVERT: A 251 TYR cc_start: 0.7373 (m-10) cc_final: 0.6889 (m-10) REVERT: A 928 PHE cc_start: 0.2124 (OUTLIER) cc_final: 0.1349 (m-10) REVERT: A 945 GLU cc_start: 0.8157 (tt0) cc_final: 0.7911 (tt0) REVERT: A 950 ASN cc_start: 0.8818 (t0) cc_final: 0.8001 (t0) REVERT: A 1186 MET cc_start: 0.8229 (mtt) cc_final: 0.7878 (mtt) outliers start: 25 outliers final: 20 residues processed: 106 average time/residue: 0.1894 time to fit residues: 30.8189 Evaluate side-chains 109 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 928 PHE Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A1257 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 = 0.4210 r_free = 0.4210 target = 0.196494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125088 restraints weight = 10527.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129321 restraints weight = 5868.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130441 restraints weight = 3895.189| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8990 Z= 0.164 Angle : 0.542 8.292 12207 Z= 0.269 Chirality : 0.042 0.162 1391 Planarity : 0.004 0.036 1523 Dihedral : 4.563 48.882 1210 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.87 % Allowed : 19.19 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.26), residues: 1088 helix: 1.07 (0.24), residues: 461 sheet: -0.50 (0.48), residues: 123 loop : -1.69 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.004 0.001 HIS A 977 PHE 0.021 0.001 PHE A1361 TYR 0.017 0.001 TYR A1317 ARG 0.003 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.928 Fit side-chains REVERT: A 945 GLU cc_start: 0.8058 (tt0) cc_final: 0.7824 (tt0) REVERT: A 950 ASN cc_start: 0.8779 (t0) cc_final: 0.7979 (t0) REVERT: A 1186 MET cc_start: 0.8112 (mtt) cc_final: 0.7767 (mtt) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1674 time to fit residues: 25.4694 Evaluate side-chains 102 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.195565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123515 restraints weight = 10517.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127144 restraints weight = 6082.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128438 restraints weight = 4158.737| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8990 Z= 0.196 Angle : 0.556 9.687 12207 Z= 0.276 Chirality : 0.042 0.154 1391 Planarity : 0.004 0.035 1523 Dihedral : 4.546 48.002 1210 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 19.81 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.49 (0.26), residues: 1088 helix: 1.08 (0.24), residues: 462 sheet: -0.53 (0.50), residues: 113 loop : -1.63 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1245 HIS 0.003 0.000 HIS A1352 PHE 0.018 0.001 PHE A 536 TYR 0.017 0.002 TYR A1182 ARG 0.002 0.000 ARG A1070 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.905 Fit side-chains REVERT: A 932 GLU cc_start: 0.7881 (pt0) cc_final: 0.7561 (pt0) REVERT: A 945 GLU cc_start: 0.8133 (tt0) cc_final: 0.7887 (tt0) REVERT: A 950 ASN cc_start: 0.8835 (t0) cc_final: 0.8015 (t0) REVERT: A 1186 MET cc_start: 0.8184 (mtt) cc_final: 0.7812 (mtt) outliers start: 16 outliers final: 16 residues processed: 99 average time/residue: 0.1712 time to fit residues: 25.9035 Evaluate side-chains 101 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.4980 chunk 100 optimal weight: 0.0020 chunk 64 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 94 optimal weight: 0.7980 chunk 54 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** 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 = 0.4223 r_free = 0.4223 target = 0.197867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125423 restraints weight = 10549.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129268 restraints weight = 5709.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131645 restraints weight = 4081.470| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8990 Z= 0.149 Angle : 0.541 8.987 12207 Z= 0.268 Chirality : 0.042 0.155 1391 Planarity : 0.004 0.039 1523 Dihedral : 4.459 46.718 1210 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.76 % Allowed : 19.92 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.33 (0.26), residues: 1088 helix: 1.26 (0.24), residues: 461 sheet: -0.49 (0.50), residues: 113 loop : -1.59 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.004 0.000 HIS A 977 PHE 0.021 0.001 PHE A1361 TYR 0.016 0.001 TYR A1317 ARG 0.002 0.000 ARG A1070 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.65 seconds wall clock time: 59 minutes 11.42 seconds (3551.42 seconds total)