Starting phenix.real_space_refine on Wed Aug 5 21:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s2h_54500/08_2026/9s2h_54500.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 7338 2.51 5 N 1825 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11263 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10857 Classifications: {'peptide': 1358} Link IDs: {'PTRANS': 49, 'TRANS': 1308} Chain breaks: 4 Chain: "A" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 406 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1, 'ERG': 11} Classifications: {'undetermined': 14, 'water': 28} Link IDs: {None: 41} Time building chain proxies: 2.51, per 1000 atoms: 0.22 Number of scatterers: 11263 At special positions: 0 Unit cell: (88.934, 107.392, 150.181, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 5 15.00 Mg 1 11.99 O 2034 8.00 N 1825 7.00 C 7338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1399 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1415 " - pdb=" SG CYS A1440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 523.2 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 57.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 89 through 102 removed outlier: 3.755A pdb=" N TRP A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.845A pdb=" N LYS A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.605A pdb=" N VAL A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.972A pdb=" N THR A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.555A pdb=" N LEU A 365 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.691A pdb=" N GLY A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.635A pdb=" N ILE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.760A pdb=" N PHE A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.797A pdb=" N MET A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 4.175A pdb=" N SER A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 584 through 615 removed outlier: 3.600A pdb=" N ASP A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.770A pdb=" N THR A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 610 " --> pdb=" O CYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 649 removed outlier: 3.724A pdb=" N PHE A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.510A pdb=" N SER A 683 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 684 " --> pdb=" O GLY A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 684' Processing helix chain 'A' and resid 685 through 690 removed outlier: 3.830A pdb=" N ILE A 689 " --> pdb=" O TRP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.837A pdb=" N TYR A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 768 through 784 removed outlier: 3.887A pdb=" N PHE A 774 " --> pdb=" O TYR A 770 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 948 through 961 Processing helix chain 'A' and resid 966 through 981 removed outlier: 3.537A pdb=" N LEU A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.036A pdb=" N GLN A 985 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 987 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1013 removed outlier: 3.587A pdb=" N GLU A1011 " --> pdb=" O THR A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1046 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.762A pdb=" N GLU A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 4.350A pdb=" N ILE A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1117 Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1136 through 1151 Processing helix chain 'A' and resid 1171 through 1189 Processing helix chain 'A' and resid 1190 through 1212 removed outlier: 4.127A pdb=" N SER A1196 " --> pdb=" O ASP A1192 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A1199 " --> pdb=" O TRP A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1232 Processing helix chain 'A' and resid 1235 through 1257 removed outlier: 3.572A pdb=" N GLN A1242 " --> pdb=" O PRO A1238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A1244 " --> pdb=" O LEU A1240 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1265 through 1273 Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 4.124A pdb=" N TRP A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1305 removed outlier: 4.180A pdb=" N ASN A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1302 " --> pdb=" O PHE A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1336 removed outlier: 4.536A pdb=" N PHE A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 removed outlier: 3.846A pdb=" N MET A1346 " --> pdb=" O ALA A1342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A1354 " --> pdb=" O MET A1350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1371 through 1378 Processing helix chain 'A' and resid 1378 through 1391 removed outlier: 4.347A pdb=" N TYR A1382 " --> pdb=" O SER A1378 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A1389 " --> pdb=" O ASP A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1419 Processing helix chain 'A' and resid 1419 through 1427 Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.815A pdb=" N PHE A1451 " --> pdb=" O HIS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1461 No H-bonds generated for 'chain 'A' and resid 1459 through 1461' Processing helix chain 'A' and resid 1462 through 1486 removed outlier: 3.832A pdb=" N TRP A1466 " --> pdb=" O ARG A1462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.617A pdb=" N ASN A 203 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 182 removed outlier: 6.406A pdb=" N VAL A 179 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 372 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU A 181 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 369 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 380 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 371 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 874 Processing sheet with id=AA6, first strand: chain 'A' and resid 879 through 883 removed outlier: 5.862A pdb=" N VAL A 879 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 861 " --> pdb=" O VAL A 879 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1019 through 1022 removed outlier: 3.649A pdb=" N LEU A1052 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1068 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A1080 " --> pdb=" O PHE A1071 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1430 through 1431 removed outlier: 3.623A pdb=" N TYR A1430 " --> pdb=" O CYS A1443 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1527 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: 2.21 Time building geometry restraints manager: 1.37 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: 3469 1.34 - 1.46: 2533 1.46 - 1.58: 5447 1.58 - 1.69: 8 1.69 - 1.81: 93 Bond restraints: 11550 Sorted by residual: bond pdb=" CB GLN A 985 " pdb=" CG GLN A 985 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.51e+00 bond pdb=" CB GLN A1140 " pdb=" CG GLN A1140 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" C4 ADP A1603 " pdb=" C5 ADP A1603 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" CA GLU A1024 " pdb=" CB GLU A1024 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.11e+00 bond pdb=" CB ILE A 129 " pdb=" CG1 ILE A 129 " ideal model delta sigma weight residual 1.530 1.550 -0.020 2.00e-02 2.50e+03 9.72e-01 ... (remaining 11545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15526 2.06 - 4.11: 163 4.11 - 6.17: 39 6.17 - 8.22: 10 8.22 - 10.28: 5 Bond angle restraints: 15743 Sorted by residual: angle pdb=" C SER A 126 " pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 116.54 110.20 6.34 1.15e+00 7.56e-01 3.03e+01 angle pdb=" C THR A 84 " pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CA GLN A 985 " pdb=" CB GLN A 985 " pdb=" CG GLN A 985 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N ASP A 741 " pdb=" CA ASP A 741 " pdb=" C ASP A 741 " ideal model delta sigma weight residual 110.80 103.14 7.66 2.13e+00 2.20e-01 1.29e+01 angle pdb=" CA SER A 126 " pdb=" C SER A 126 " pdb=" N ALA A 127 " ideal model delta sigma weight residual 119.52 116.70 2.82 7.90e-01 1.60e+00 1.27e+01 ... (remaining 15738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6313 18.01 - 36.01: 742 36.01 - 54.02: 205 54.02 - 72.03: 67 72.03 - 90.03: 2 Dihedral angle restraints: 7329 sinusoidal: 3360 harmonic: 3969 Sorted by residual: dihedral pdb=" CB CYS A 711 " pdb=" SG CYS A 711 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -157.83 71.83 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" C5' ADP A1603 " pdb=" O5' ADP A1603 " pdb=" PA ADP A1603 " pdb=" O2A ADP A1603 " ideal model delta sinusoidal sigma weight residual -60.00 30.03 -90.03 1 2.00e+01 2.50e-03 2.40e+01 dihedral pdb=" CB CYS A1415 " pdb=" SG CYS A1415 " pdb=" SG CYS A1440 " pdb=" CB CYS A1440 " ideal model delta sinusoidal sigma weight residual -86.00 -124.41 38.41 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 7326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1442 0.052 - 0.104: 254 0.104 - 0.155: 38 0.155 - 0.207: 4 0.207 - 0.259: 4 Chirality restraints: 1742 Sorted by residual: chirality pdb=" C20 ERG A1609 " pdb=" C17 ERG A1609 " pdb=" C21 ERG A1609 " pdb=" C22 ERG A1609 " both_signs ideal model delta sigma weight residual False 2.58 2.32 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C20 ERG A1614 " pdb=" C17 ERG A1614 " pdb=" C21 ERG A1614 " pdb=" C22 ERG A1614 " both_signs ideal model delta sigma weight residual False 2.58 2.33 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C17 ERG A1609 " pdb=" C13 ERG A1609 " pdb=" C16 ERG A1609 " pdb=" C20 ERG A1609 " both_signs ideal model delta sigma weight residual False 2.59 2.37 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1739 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1148 " 0.009 2.00e-02 2.50e+03 1.13e-02 3.19e+00 pdb=" CG TRP A1148 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A1148 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1148 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1148 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1148 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1148 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 597 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 598 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 129 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ILE A 129 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 129 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 130 " 0.010 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 113 2.59 - 3.17: 9309 3.17 - 3.74: 17618 3.74 - 4.32: 24591 4.32 - 4.90: 40782 Nonbonded interactions: 92413 Sorted by model distance: nonbonded pdb="MG MG A1602 " pdb=" O1B ADP A1603 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR A 900 " pdb="MG MG A1602 " model vdw 2.086 2.170 nonbonded pdb=" CG PRO A 105 " pdb=" ND2 ASN A 258 " model vdw 2.154 3.520 nonbonded pdb=" OE1 GLU A1024 " pdb=" OG SER A1027 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG A1311 " pdb=" O GLY A1391 " model vdw 2.240 3.120 ... (remaining 92408 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=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.003 0.048 11554 Z= 0.115 Angle : 0.602 10.277 15749 Z= 0.293 Chirality : 0.041 0.259 1742 Planarity : 0.004 0.044 1926 Dihedral : 16.442 90.032 4776 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 1.96 % Allowed : 25.40 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1348 helix: 0.19 (0.20), residues: 704 sheet: -1.98 (0.51), residues: 86 loop : -1.36 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.015 0.001 TYR A 131 PHE 0.016 0.001 PHE A 764 TRP 0.030 0.001 TRP A1148 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (11550) covalent geometry : angle 0.60211 / 0.29 (15743) SS BOND : bond 0.00059 / 0.03 ( 3) SS BOND : angle 0.82959 / 0.43 ( 6) hydrogen bonds : bond 0.22811 / 15.11 ( 524) hydrogen bonds : angle 7.41436 / 5.22 ( 1527) Misc. bond : bond 0.00196 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.483 Fit side-chains REVERT: A 31 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 522 MET cc_start: 0.7251 (mmt) cc_final: 0.6929 (mmt) REVERT: A 791 LYS cc_start: 0.7614 (mttt) cc_final: 0.6802 (ptpp) outliers start: 23 outliers final: 18 residues processed: 137 average time/residue: 0.1170 time to fit residues: 23.1804 Evaluate side-chains 137 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 134 ASN A 608 ASN A 631 ASN A 759 HIS A 961 GLN A1032 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108291 restraints weight = 15946.259| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.14 r_work: 0.3134 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11554 Z= 0.122 Angle : 0.602 9.617 15749 Z= 0.294 Chirality : 0.042 0.257 1742 Planarity : 0.004 0.043 1926 Dihedral : 9.683 84.043 2300 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 2.81 % Allowed : 22.59 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.23), residues: 1348 helix: 0.72 (0.19), residues: 724 sheet: -1.56 (0.51), residues: 92 loop : -1.40 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 643 TYR 0.009 0.001 TYR A 986 PHE 0.012 0.001 PHE A 336 TRP 0.016 0.001 TRP A1195 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11550) covalent geometry : angle 0.60196 / 0.29 (15743) SS BOND : bond 0.00229 / 0.12 ( 3) SS BOND : angle 0.45675 / 0.22 ( 6) hydrogen bonds : bond 0.05117 / 3.46 ( 524) hydrogen bonds : angle 4.65639 / 3.31 ( 1527) Misc. bond : bond 0.00134 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 31 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: A 451 LYS cc_start: 0.8715 (mttp) cc_final: 0.8290 (mtpt) REVERT: A 522 MET cc_start: 0.8620 (mmt) cc_final: 0.8394 (mmt) REVERT: A 638 MET cc_start: 0.8222 (mmp) cc_final: 0.7759 (mmp) REVERT: A 783 GLU cc_start: 0.8308 (pp20) cc_final: 0.7383 (tt0) REVERT: A 791 LYS cc_start: 0.7954 (mttt) cc_final: 0.7509 (ptpp) REVERT: A 940 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 942 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7592 (pp) REVERT: A 985 GLN cc_start: 0.8766 (tp40) cc_final: 0.8241 (tm-30) REVERT: A 1001 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: A 1051 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 1149 MET cc_start: 0.7882 (mtp) cc_final: 0.7546 (mtm) REVERT: A 1258 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: A 1352 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (t) outliers start: 33 outliers final: 17 residues processed: 158 average time/residue: 0.1028 time to fit residues: 24.2583 Evaluate side-chains 143 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 0.0270 chunk 86 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 258 ASN A 722 ASN A 877 ASN ** A1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111468 restraints weight = 16003.498| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.08 r_work: 0.3184 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11554 Z= 0.119 Angle : 0.576 9.532 15749 Z= 0.278 Chirality : 0.042 0.265 1742 Planarity : 0.004 0.044 1926 Dihedral : 9.524 71.578 2290 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 3.58 % Allowed : 21.99 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1348 helix: 0.88 (0.19), residues: 730 sheet: -1.35 (0.52), residues: 92 loop : -1.42 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.009 0.001 TYR A 627 PHE 0.014 0.001 PHE A 336 TRP 0.009 0.001 TRP A 117 HIS 0.003 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11550) covalent geometry : angle 0.57595 / 0.28 (15743) SS BOND : bond 0.00167 / 0.09 ( 3) SS BOND : angle 0.58258 / 0.29 ( 6) hydrogen bonds : bond 0.04339 / 2.94 ( 524) hydrogen bonds : angle 4.25786 / 3.02 ( 1527) Misc. bond : bond 0.00151 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.485 Fit side-chains REVERT: A 31 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: A 451 LYS cc_start: 0.8637 (mttp) cc_final: 0.8270 (mtpt) REVERT: A 638 MET cc_start: 0.8237 (mmp) cc_final: 0.7858 (mmp) REVERT: A 783 GLU cc_start: 0.8313 (pp20) cc_final: 0.7473 (tt0) REVERT: A 791 LYS cc_start: 0.7933 (mttt) cc_final: 0.7621 (ptpp) REVERT: A 940 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: A 942 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7718 (pp) REVERT: A 985 GLN cc_start: 0.8770 (tp40) cc_final: 0.8274 (tm-30) REVERT: A 1001 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: A 1017 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8505 (tttm) REVERT: A 1051 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8496 (mm) REVERT: A 1149 MET cc_start: 0.7784 (mtp) cc_final: 0.7493 (mtm) REVERT: A 1258 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8607 (mt-10) outliers start: 42 outliers final: 21 residues processed: 154 average time/residue: 0.1072 time to fit residues: 24.5256 Evaluate side-chains 143 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 97 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 343 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 GLN ** 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 = 0.3620 r_free = 0.3620 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110654 restraints weight = 16031.051| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.05 r_work: 0.3162 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11554 Z= 0.136 Angle : 0.584 9.527 15749 Z= 0.280 Chirality : 0.042 0.266 1742 Planarity : 0.004 0.045 1926 Dihedral : 9.380 70.023 2285 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 3.67 % Allowed : 22.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1348 helix: 0.91 (0.19), residues: 732 sheet: -1.34 (0.52), residues: 92 loop : -1.39 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.009 0.001 TYR A 627 PHE 0.014 0.001 PHE A 336 TRP 0.013 0.001 TRP A1148 HIS 0.004 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11550) covalent geometry : angle 0.58360 / 0.28 (15743) SS BOND : bond 0.00415 / 0.22 ( 3) SS BOND : angle 0.67451 / 0.34 ( 6) hydrogen bonds : bond 0.04162 / 2.82 ( 524) hydrogen bonds : angle 4.10801 / 2.92 ( 1527) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.566 Fit side-chains REVERT: A 31 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: A 423 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8716 (pt) REVERT: A 451 LYS cc_start: 0.8608 (mttp) cc_final: 0.8237 (mtpt) REVERT: A 638 MET cc_start: 0.8256 (mmp) cc_final: 0.7864 (mmp) REVERT: A 783 GLU cc_start: 0.8318 (pp20) cc_final: 0.7552 (tt0) REVERT: A 791 LYS cc_start: 0.7970 (mttt) cc_final: 0.7648 (ptpp) REVERT: A 940 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: A 942 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7810 (pp) REVERT: A 979 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8282 (mmmm) REVERT: A 985 GLN cc_start: 0.8805 (tp40) cc_final: 0.8288 (tm-30) REVERT: A 1001 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: A 1017 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8490 (tttm) REVERT: A 1063 MET cc_start: 0.8380 (tmm) cc_final: 0.8160 (ttt) REVERT: A 1149 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7648 (mtm) REVERT: A 1258 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8610 (mt-10) outliers start: 43 outliers final: 24 residues processed: 153 average time/residue: 0.1211 time to fit residues: 26.9460 Evaluate side-chains 148 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1149 MET Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 29 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 198 ASN A 258 ASN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111404 restraints weight = 15857.677| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.02 r_work: 0.3173 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11554 Z= 0.145 Angle : 0.589 9.574 15749 Z= 0.284 Chirality : 0.043 0.267 1742 Planarity : 0.004 0.046 1926 Dihedral : 9.339 72.560 2283 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 3.67 % Allowed : 22.68 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1348 helix: 0.94 (0.19), residues: 731 sheet: -1.23 (0.53), residues: 92 loop : -1.42 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.009 0.001 TYR A 627 PHE 0.018 0.001 PHE A 764 TRP 0.015 0.001 TRP A1148 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (11550) covalent geometry : angle 0.58939 / 0.28 (15743) SS BOND : bond 0.00240 / 0.12 ( 3) SS BOND : angle 0.70125 / 0.35 ( 6) hydrogen bonds : bond 0.04112 / 2.79 ( 524) hydrogen bonds : angle 4.02568 / 2.85 ( 1527) Misc. bond : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.439 Fit side-chains REVERT: A 31 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 451 LYS cc_start: 0.8588 (mttp) cc_final: 0.8221 (mtpt) REVERT: A 638 MET cc_start: 0.8300 (mmp) cc_final: 0.7927 (mmp) REVERT: A 783 GLU cc_start: 0.8273 (pp20) cc_final: 0.7568 (tt0) REVERT: A 791 LYS cc_start: 0.7988 (mttt) cc_final: 0.7682 (ptpp) REVERT: A 940 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: A 942 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7817 (pp) REVERT: A 979 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8340 (mmmm) REVERT: A 985 GLN cc_start: 0.8841 (tp40) cc_final: 0.8290 (tm-30) REVERT: A 1001 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: A 1017 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8525 (tttm) REVERT: A 1063 MET cc_start: 0.8392 (tmm) cc_final: 0.8188 (ttt) REVERT: A 1149 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7746 (mtm) REVERT: A 1239 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8903 (mp) REVERT: A 1258 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8600 (mt-10) outliers start: 43 outliers final: 27 residues processed: 161 average time/residue: 0.1061 time to fit residues: 25.0015 Evaluate side-chains 157 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1149 MET Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 GLN ** 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 = 0.3638 r_free = 0.3638 target = 0.136540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111753 restraints weight = 16100.909| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.07 r_work: 0.3189 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11554 Z= 0.123 Angle : 0.573 9.457 15749 Z= 0.275 Chirality : 0.042 0.264 1742 Planarity : 0.004 0.046 1926 Dihedral : 9.261 69.876 2283 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 3.32 % Allowed : 22.93 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1348 helix: 1.01 (0.19), residues: 732 sheet: -1.24 (0.52), residues: 92 loop : -1.36 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1182 TYR 0.009 0.001 TYR A 627 PHE 0.017 0.001 PHE A 764 TRP 0.016 0.001 TRP A1148 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (11550) covalent geometry : angle 0.57256 / 0.27 (15743) SS BOND : bond 0.00118 / 0.06 ( 3) SS BOND : angle 0.70883 / 0.36 ( 6) hydrogen bonds : bond 0.03846 / 2.61 ( 524) hydrogen bonds : angle 3.94558 / 2.79 ( 1527) Misc. bond : bond 0.00156 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.414 Fit side-chains REVERT: A 31 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: A 638 MET cc_start: 0.8295 (mmp) cc_final: 0.7966 (mmp) REVERT: A 783 GLU cc_start: 0.8259 (pp20) cc_final: 0.7583 (mt-10) REVERT: A 791 LYS cc_start: 0.7975 (mttt) cc_final: 0.7681 (ptpp) REVERT: A 940 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: A 942 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7877 (pp) REVERT: A 979 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8268 (mmmm) REVERT: A 985 GLN cc_start: 0.8860 (tp40) cc_final: 0.8284 (tm-30) REVERT: A 1001 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: A 1017 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8492 (tttm) REVERT: A 1063 MET cc_start: 0.8401 (tmm) cc_final: 0.8186 (ttt) REVERT: A 1149 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7788 (mtm) REVERT: A 1239 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 1258 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8584 (mt-10) outliers start: 39 outliers final: 24 residues processed: 154 average time/residue: 0.0998 time to fit residues: 22.2220 Evaluate side-chains 151 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1149 MET Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 34 optimal weight: 0.0170 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 258 ASN A1205 ASN ** A1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112437 restraints weight = 15998.209| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11554 Z= 0.116 Angle : 0.567 9.404 15749 Z= 0.273 Chirality : 0.042 0.265 1742 Planarity : 0.004 0.046 1926 Dihedral : 9.122 68.512 2283 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 3.58 % Allowed : 22.68 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.24), residues: 1348 helix: 1.10 (0.19), residues: 732 sheet: -1.12 (0.52), residues: 92 loop : -1.35 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.010 0.001 TYR A 627 PHE 0.017 0.001 PHE A 764 TRP 0.019 0.001 TRP A1148 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11550) covalent geometry : angle 0.56736 / 0.27 (15743) SS BOND : bond 0.00231 / 0.12 ( 3) SS BOND : angle 0.72383 / 0.37 ( 6) hydrogen bonds : bond 0.03679 / 2.50 ( 524) hydrogen bonds : angle 3.85751 / 2.72 ( 1527) Misc. bond : bond 0.00154 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.323 Fit side-chains REVERT: A 31 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: A 638 MET cc_start: 0.8292 (mmp) cc_final: 0.7981 (mmp) REVERT: A 783 GLU cc_start: 0.8228 (pp20) cc_final: 0.7558 (mt-10) REVERT: A 791 LYS cc_start: 0.7978 (mttt) cc_final: 0.7643 (ptpp) REVERT: A 940 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: A 942 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7836 (pp) REVERT: A 1001 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: A 1017 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8453 (tttm) REVERT: A 1063 MET cc_start: 0.8378 (tmm) cc_final: 0.8172 (ttt) REVERT: A 1140 GLN cc_start: 0.8235 (tp40) cc_final: 0.7810 (tm-30) REVERT: A 1239 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 1258 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8610 (mt-10) outliers start: 42 outliers final: 29 residues processed: 161 average time/residue: 0.0954 time to fit residues: 22.4440 Evaluate side-chains 156 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A1032 GLN A1057 GLN A1186 GLN ** A1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112257 restraints weight = 15950.864| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.05 r_work: 0.3198 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11554 Z= 0.128 Angle : 0.593 10.204 15749 Z= 0.287 Chirality : 0.042 0.266 1742 Planarity : 0.004 0.046 1926 Dihedral : 9.142 68.329 2283 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 3.41 % Allowed : 22.68 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1348 helix: 1.16 (0.19), residues: 726 sheet: -1.10 (0.52), residues: 92 loop : -1.40 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.009 0.001 TYR A 627 PHE 0.016 0.001 PHE A 764 TRP 0.019 0.001 TRP A1148 HIS 0.005 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11550) covalent geometry : angle 0.59309 / 0.29 (15743) SS BOND : bond 0.00115 / 0.06 ( 3) SS BOND : angle 0.79177 / 0.42 ( 6) hydrogen bonds : bond 0.03751 / 2.54 ( 524) hydrogen bonds : angle 3.86069 / 2.72 ( 1527) Misc. bond : bond 0.00146 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.339 Fit side-chains REVERT: A 31 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: A 638 MET cc_start: 0.8293 (mmp) cc_final: 0.7974 (mmp) REVERT: A 783 GLU cc_start: 0.8249 (pp20) cc_final: 0.7577 (mt-10) REVERT: A 791 LYS cc_start: 0.7935 (mttt) cc_final: 0.7639 (ptpp) REVERT: A 940 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 942 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7859 (pp) REVERT: A 979 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8276 (mmmm) REVERT: A 1001 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: A 1017 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8449 (tttm) REVERT: A 1063 MET cc_start: 0.8395 (tmm) cc_final: 0.8190 (ttt) REVERT: A 1149 MET cc_start: 0.7206 (mtm) cc_final: 0.6747 (mtm) REVERT: A 1239 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 1258 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8589 (mt-10) outliers start: 40 outliers final: 29 residues processed: 152 average time/residue: 0.0957 time to fit residues: 21.2396 Evaluate side-chains 157 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1086 ASP Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A 507 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.132015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107358 restraints weight = 16129.429| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.04 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11554 Z= 0.250 Angle : 0.683 9.824 15749 Z= 0.334 Chirality : 0.047 0.273 1742 Planarity : 0.004 0.049 1926 Dihedral : 9.710 81.723 2283 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 3.41 % Allowed : 22.76 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1348 helix: 0.78 (0.19), residues: 732 sheet: -1.34 (0.52), residues: 92 loop : -1.54 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1182 TYR 0.016 0.002 TYR A1193 PHE 0.021 0.002 PHE A 764 TRP 0.026 0.002 TRP A1148 HIS 0.007 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (11550) covalent geometry : angle 0.68237 / 0.33 (15743) SS BOND : bond 0.00307 / 0.16 ( 3) SS BOND : angle 1.16099 / 0.62 ( 6) hydrogen bonds : bond 0.04776 / 3.23 ( 524) hydrogen bonds : angle 4.11839 / 2.91 ( 1527) Misc. bond : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.417 Fit side-chains REVERT: A 31 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 638 MET cc_start: 0.8408 (mmp) cc_final: 0.8016 (mmp) REVERT: A 783 GLU cc_start: 0.8250 (pp20) cc_final: 0.7598 (mt-10) REVERT: A 791 LYS cc_start: 0.8008 (mttt) cc_final: 0.7714 (ptpp) REVERT: A 940 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: A 942 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8014 (pp) REVERT: A 979 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (mmmm) REVERT: A 1001 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: A 1017 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8580 (tttm) REVERT: A 1140 GLN cc_start: 0.8205 (tp40) cc_final: 0.7880 (tm-30) REVERT: A 1258 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8625 (mt-10) outliers start: 40 outliers final: 30 residues processed: 146 average time/residue: 0.0909 time to fit residues: 19.2768 Evaluate side-chains 152 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1113 MET Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A1225 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.136597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112170 restraints weight = 15944.046| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.03 r_work: 0.3189 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11554 Z= 0.118 Angle : 0.598 9.449 15749 Z= 0.288 Chirality : 0.042 0.271 1742 Planarity : 0.004 0.045 1926 Dihedral : 9.248 72.469 2283 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 2.64 % Allowed : 23.61 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1348 helix: 1.06 (0.20), residues: 727 sheet: -1.23 (0.51), residues: 92 loop : -1.43 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.007 0.001 TYR A 627 PHE 0.013 0.001 PHE A 764 TRP 0.021 0.001 TRP A1148 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11550) covalent geometry : angle 0.59763 / 0.29 (15743) SS BOND : bond 0.00380 / 0.20 ( 3) SS BOND : angle 1.01982 / 0.53 ( 6) hydrogen bonds : bond 0.03758 / 2.55 ( 524) hydrogen bonds : angle 3.91498 / 2.75 ( 1527) Misc. bond : bond 0.00144 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.262 Fit side-chains REVERT: A 31 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: A 638 MET cc_start: 0.8294 (mmp) cc_final: 0.7979 (mmp) REVERT: A 783 GLU cc_start: 0.8234 (pp20) cc_final: 0.7581 (mt-10) REVERT: A 791 LYS cc_start: 0.7953 (mttt) cc_final: 0.7617 (ptpp) REVERT: A 940 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 942 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7895 (pp) REVERT: A 979 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: A 1001 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: A 1017 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8478 (tttm) REVERT: A 1140 GLN cc_start: 0.8142 (tp40) cc_final: 0.7823 (tm-30) REVERT: A 1152 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8306 (mm-30) REVERT: A 1258 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8614 (mt-10) outliers start: 31 outliers final: 22 residues processed: 151 average time/residue: 0.0916 time to fit residues: 20.2990 Evaluate side-chains 153 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1165 HIS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1258 GLU Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A1225 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.137689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113300 restraints weight = 15932.472| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.05 r_work: 0.3210 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11554 Z= 0.108 Angle : 0.579 9.291 15749 Z= 0.278 Chirality : 0.041 0.265 1742 Planarity : 0.004 0.045 1926 Dihedral : 9.015 68.021 2283 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.81 % Allowed : 23.61 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1348 helix: 1.24 (0.20), residues: 726 sheet: -1.10 (0.52), residues: 92 loop : -1.43 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1134 TYR 0.010 0.001 TYR A 627 PHE 0.012 0.001 PHE A 336 TRP 0.025 0.001 TRP A1148 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11550) covalent geometry : angle 0.57912 / 0.28 (15743) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 0.85489 / 0.44 ( 6) hydrogen bonds : bond 0.03502 / 2.38 ( 524) hydrogen bonds : angle 3.82532 / 2.68 ( 1527) Misc. bond : bond 0.00140 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.01 seconds wall clock time: 50 minutes 16.20 seconds (3016.20 seconds total)