Starting phenix.real_space_refine on Sat Aug 23 10:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2025/8sfi_40442.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 23 5.16 5 C 7114 2.51 5 N 1952 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1227, 10030 Classifications: {'peptide': 1227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1180} Chain breaks: 3 Chain: "B" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 21} Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 2.55, per 1000 atoms: 0.22 Number of scatterers: 11477 At special positions: 0 Unit cell: (98.294, 100.793, 147.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 69 15.00 O 2319 8.00 N 1952 7.00 C 7114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 339.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 54.4% alpha, 10.4% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.692A pdb=" N GLU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.694A pdb=" N SER A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 111 removed outlier: 3.857A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.408A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.545A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.745A pdb=" N LYS A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.904A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.932A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.685A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.570A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.840A pdb=" N SER A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 402 through 415 removed outlier: 4.161A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.688A pdb=" N LYS A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.509A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.899A pdb=" N MET A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.506A pdb=" N MET A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 621 removed outlier: 3.583A pdb=" N GLN A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.555A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.660A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 685 removed outlier: 3.855A pdb=" N SER A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.617A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.861A pdb=" N ALA A 751 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.580A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 865 removed outlier: 3.584A pdb=" N THR A 865 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 954 removed outlier: 3.502A pdb=" N VAL A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.936A pdb=" N GLY A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 963 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 4.009A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1189 Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 3.964A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.603A pdb=" N SER A1284 " --> pdb=" O HIS A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1306 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.492A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 593 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.492A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA5, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931 removed outlier: 4.333A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG A 909 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A1065 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1107 removed outlier: 3.980A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1165 removed outlier: 6.612A pdb=" N ARG A1159 " --> pdb=" O ARG A1174 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A1174 " --> pdb=" O ARG A1159 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1161 " --> pdb=" O ARG A1172 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG A1172 " --> pdb=" O VAL A1161 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A1163 " --> pdb=" O THR A1170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1228 506 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2956 1.34 - 1.46: 2772 1.46 - 1.58: 5970 1.58 - 1.70: 138 1.70 - 1.82: 38 Bond restraints: 11874 Sorted by residual: bond pdb=" CB PRO A 648 " pdb=" CG PRO A 648 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " ideal model delta sigma weight residual 1.520 1.601 -0.081 3.00e-02 1.11e+03 7.24e+00 bond pdb=" CB LYS A 965 " pdb=" CG LYS A 965 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ARG A 411 " pdb=" CG ARG A 411 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.24e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 15964 2.71 - 5.42: 251 5.42 - 8.13: 64 8.13 - 10.84: 55 10.84 - 13.55: 13 Bond angle restraints: 16347 Sorted by residual: angle pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" CD PRO A 648 " ideal model delta sigma weight residual 112.00 98.45 13.55 1.40e+00 5.10e-01 9.37e+01 angle pdb=" N ASP A 939 " pdb=" CA ASP A 939 " pdb=" C ASP A 939 " ideal model delta sigma weight residual 110.24 118.36 -8.12 1.30e+00 5.92e-01 3.90e+01 angle pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " pdb=" CD LYS A 468 " ideal model delta sigma weight residual 111.30 123.87 -12.57 2.30e+00 1.89e-01 2.99e+01 angle pdb=" C PHE A 938 " pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " ideal model delta sigma weight residual 111.74 120.37 -8.63 1.59e+00 3.96e-01 2.95e+01 angle pdb=" CA LYS A1109 " pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 ... (remaining 16342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 6491 30.65 - 61.29: 550 61.29 - 91.94: 38 91.94 - 122.58: 0 122.58 - 153.23: 2 Dihedral angle restraints: 7081 sinusoidal: 3463 harmonic: 3618 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 46.77 153.23 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 53.50 146.50 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" CA THR A 522 " pdb=" C THR A 522 " pdb=" N LYS A 523 " pdb=" CA LYS A 523 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 7078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1695 0.104 - 0.208: 100 0.208 - 0.311: 6 0.311 - 0.415: 11 0.415 - 0.519: 4 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CG LEU A 471 " pdb=" CB LEU A 471 " pdb=" CD1 LEU A 471 " pdb=" CD2 LEU A 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1813 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A 606 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 537 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 538 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 647 " -0.065 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 648 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.049 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1305 2.75 - 3.29: 11003 3.29 - 3.83: 20297 3.83 - 4.36: 23053 4.36 - 4.90: 38033 Nonbonded interactions: 93691 Sorted by model distance: nonbonded pdb=" O GLU A 441 " pdb=" OG SER A 444 " model vdw 2.218 3.040 nonbonded pdb=" O ASN A1090 " pdb=" OG SER A1093 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 11 " pdb=" OD1 ASN A1024 " model vdw 2.290 3.040 nonbonded pdb=" O GLN A 437 " pdb=" OG SER A 440 " model vdw 2.299 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.300 3.040 ... (remaining 93686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.010 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.920 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 11874 Z= 0.213 Angle : 1.079 13.549 16347 Z= 0.527 Chirality : 0.063 0.519 1816 Planarity : 0.008 0.132 1852 Dihedral : 19.823 153.226 4739 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.46 % Allowed : 24.27 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.23), residues: 1219 helix: -0.55 (0.20), residues: 589 sheet: -0.85 (0.42), residues: 148 loop : -0.59 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 160 TYR 0.030 0.002 TYR A 746 PHE 0.049 0.003 PHE A1117 TRP 0.028 0.002 TRP A1085 HIS 0.006 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00490 (11874) covalent geometry : angle 1.07862 (16347) hydrogen bonds : bond 0.13099 ( 561) hydrogen bonds : angle 5.87020 ( 1543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 THR cc_start: 0.8148 (m) cc_final: 0.7882 (t) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.0890 time to fit residues: 13.2737 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 1192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.038834 restraints weight = 66119.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040029 restraints weight = 31069.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.040748 restraints weight = 20240.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.041153 restraints weight = 16005.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.041374 restraints weight = 14163.276| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11874 Z= 0.118 Angle : 0.595 8.609 16347 Z= 0.306 Chirality : 0.040 0.233 1816 Planarity : 0.005 0.074 1852 Dihedral : 18.170 149.623 2219 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.19 % Allowed : 20.71 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.24), residues: 1219 helix: 0.78 (0.21), residues: 612 sheet: -0.82 (0.42), residues: 150 loop : -0.37 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.012 0.001 TYR A 764 PHE 0.023 0.001 PHE A 496 TRP 0.011 0.001 TRP A1085 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00262 (11874) covalent geometry : angle 0.59468 (16347) hydrogen bonds : bond 0.03380 ( 561) hydrogen bonds : angle 4.33776 ( 1543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7606 (tpt) cc_final: 0.7271 (tpt) REVERT: A 177 LYS cc_start: 0.9689 (ttmt) cc_final: 0.9379 (mtmm) REVERT: A 507 MET cc_start: 0.9305 (ppp) cc_final: 0.9098 (ppp) REVERT: A 600 ASP cc_start: 0.8312 (t0) cc_final: 0.7871 (t0) REVERT: A 604 MET cc_start: 0.9198 (mmm) cc_final: 0.8997 (mmm) REVERT: A 619 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9145 (m-10) REVERT: A 908 ASP cc_start: 0.7997 (t0) cc_final: 0.7559 (t0) REVERT: A 1013 GLN cc_start: 0.9475 (mt0) cc_final: 0.9150 (mt0) REVERT: A 1018 MET cc_start: 0.9430 (mtm) cc_final: 0.8986 (mtm) REVERT: A 1260 MET cc_start: 0.8996 (mmt) cc_final: 0.8792 (mmm) outliers start: 24 outliers final: 10 residues processed: 90 average time/residue: 0.0807 time to fit residues: 11.4376 Evaluate side-chains 71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.050985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.034184 restraints weight = 69283.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035241 restraints weight = 33110.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.035884 restraints weight = 22129.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036227 restraints weight = 17756.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036420 restraints weight = 15758.511| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11874 Z= 0.295 Angle : 0.661 8.544 16347 Z= 0.355 Chirality : 0.043 0.144 1816 Planarity : 0.004 0.056 1852 Dihedral : 18.586 150.715 2218 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 3.56 % Allowed : 19.43 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1219 helix: 1.37 (0.21), residues: 624 sheet: -0.77 (0.42), residues: 157 loop : 0.06 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 681 TYR 0.018 0.002 TYR A 61 PHE 0.020 0.002 PHE A 496 TRP 0.020 0.002 TRP A 544 HIS 0.006 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00624 (11874) covalent geometry : angle 0.66086 (16347) hydrogen bonds : bond 0.04348 ( 561) hydrogen bonds : angle 4.35151 ( 1543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 45 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 51 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9083 (tttt) REVERT: A 507 MET cc_start: 0.9356 (ppp) cc_final: 0.8985 (ppp) REVERT: A 600 ASP cc_start: 0.9114 (t0) cc_final: 0.8756 (t0) REVERT: A 604 MET cc_start: 0.9289 (mmm) cc_final: 0.9077 (mmm) REVERT: A 908 ASP cc_start: 0.8326 (t0) cc_final: 0.7830 (t0) REVERT: A 911 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: A 1013 GLN cc_start: 0.9511 (mt0) cc_final: 0.9192 (mt0) REVERT: A 1017 LYS cc_start: 0.9528 (tptm) cc_final: 0.9285 (tptm) REVERT: A 1225 MET cc_start: 0.8968 (mmm) cc_final: 0.8460 (mmm) outliers start: 39 outliers final: 20 residues processed: 80 average time/residue: 0.0844 time to fit residues: 10.3863 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 0.0000 chunk 44 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 447 HIS ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN A1307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036574 restraints weight = 67234.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037697 restraints weight = 32216.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038383 restraints weight = 21261.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038759 restraints weight = 16846.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038886 restraints weight = 14951.446| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11874 Z= 0.107 Angle : 0.549 13.570 16347 Z= 0.281 Chirality : 0.039 0.151 1816 Planarity : 0.004 0.047 1852 Dihedral : 18.368 149.644 2218 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.83 % Allowed : 20.80 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1219 helix: 1.73 (0.22), residues: 612 sheet: -0.64 (0.41), residues: 154 loop : -0.00 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.010 0.001 TYR A 61 PHE 0.015 0.001 PHE A 496 TRP 0.013 0.001 TRP A1085 HIS 0.003 0.000 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00229 (11874) covalent geometry : angle 0.54882 (16347) hydrogen bonds : bond 0.03027 ( 561) hydrogen bonds : angle 3.92989 ( 1543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 307 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8397 (ptmm) REVERT: A 507 MET cc_start: 0.9385 (ppp) cc_final: 0.8883 (ppp) REVERT: A 600 ASP cc_start: 0.8852 (t0) cc_final: 0.8320 (t70) REVERT: A 786 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 908 ASP cc_start: 0.8336 (t0) cc_final: 0.7883 (t0) REVERT: A 1013 GLN cc_start: 0.9472 (mt0) cc_final: 0.9072 (mt0) REVERT: A 1017 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9232 (tptm) REVERT: A 1225 MET cc_start: 0.8950 (mmm) cc_final: 0.8681 (mmm) REVERT: A 1289 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (mm) outliers start: 31 outliers final: 16 residues processed: 70 average time/residue: 0.0990 time to fit residues: 10.3610 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 206 HIS A 534 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.048840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031997 restraints weight = 73270.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.033010 restraints weight = 35637.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.033578 restraints weight = 24160.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.033885 restraints weight = 19657.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.033997 restraints weight = 17596.439| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 11874 Z= 0.456 Angle : 0.786 8.555 16347 Z= 0.418 Chirality : 0.046 0.143 1816 Planarity : 0.005 0.047 1852 Dihedral : 18.794 155.974 2218 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 4.56 % Allowed : 18.89 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1219 helix: 1.37 (0.21), residues: 614 sheet: -1.07 (0.40), residues: 159 loop : 0.04 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1306 TYR 0.023 0.002 TYR A 61 PHE 0.019 0.002 PHE A 201 TRP 0.027 0.003 TRP A 544 HIS 0.010 0.002 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00960 (11874) covalent geometry : angle 0.78623 (16347) hydrogen bonds : bond 0.05309 ( 561) hydrogen bonds : angle 4.60164 ( 1543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 39 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.9397 (ppp) cc_final: 0.9167 (ppp) REVERT: A 534 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.8670 (t0) REVERT: A 544 TRP cc_start: 0.9517 (OUTLIER) cc_final: 0.8444 (m100) REVERT: A 600 ASP cc_start: 0.9328 (t0) cc_final: 0.8993 (t0) REVERT: A 908 ASP cc_start: 0.8377 (t0) cc_final: 0.7892 (t0) REVERT: A 956 GLN cc_start: 0.9571 (mm-40) cc_final: 0.9021 (tm-30) REVERT: A 1055 MET cc_start: 0.8797 (mpp) cc_final: 0.8538 (mpp) REVERT: A 1306 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.9241 (mmt-90) outliers start: 50 outliers final: 27 residues processed: 82 average time/residue: 0.0897 time to fit residues: 11.0367 Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 34 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1245 ASN Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1306 ARG Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034719 restraints weight = 69102.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035834 restraints weight = 32259.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036440 restraints weight = 21299.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036808 restraints weight = 16980.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036934 restraints weight = 15090.288| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11874 Z= 0.133 Angle : 0.585 9.047 16347 Z= 0.301 Chirality : 0.040 0.148 1816 Planarity : 0.004 0.044 1852 Dihedral : 18.600 152.958 2218 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 21.17 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1219 helix: 1.80 (0.22), residues: 616 sheet: -0.81 (0.41), residues: 154 loop : 0.10 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1306 TYR 0.015 0.001 TYR A 61 PHE 0.016 0.001 PHE A 496 TRP 0.016 0.001 TRP A1085 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00296 (11874) covalent geometry : angle 0.58458 (16347) hydrogen bonds : bond 0.03265 ( 561) hydrogen bonds : angle 4.03752 ( 1543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 307 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8406 (ptmm) REVERT: A 507 MET cc_start: 0.9433 (ppp) cc_final: 0.8888 (ppp) REVERT: A 537 MET cc_start: 0.9085 (mmm) cc_final: 0.8851 (mmm) REVERT: A 600 ASP cc_start: 0.9196 (t0) cc_final: 0.8828 (t0) REVERT: A 604 MET cc_start: 0.9391 (mmm) cc_final: 0.8753 (mmm) REVERT: A 908 ASP cc_start: 0.8461 (t0) cc_final: 0.8003 (t0) REVERT: A 956 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9051 (tm-30) REVERT: A 1055 MET cc_start: 0.8714 (mpp) cc_final: 0.8437 (mpp) outliers start: 25 outliers final: 19 residues processed: 64 average time/residue: 0.0805 time to fit residues: 8.5058 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.051028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.034158 restraints weight = 70494.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035243 restraints weight = 33331.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035876 restraints weight = 22235.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.036218 restraints weight = 17839.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036345 restraints weight = 15874.739| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11874 Z= 0.174 Angle : 0.574 12.660 16347 Z= 0.297 Chirality : 0.040 0.148 1816 Planarity : 0.003 0.043 1852 Dihedral : 18.487 151.837 2218 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.19 % Allowed : 21.26 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.25), residues: 1219 helix: 1.89 (0.22), residues: 617 sheet: -0.79 (0.42), residues: 154 loop : 0.17 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1306 TYR 0.016 0.001 TYR A 61 PHE 0.015 0.001 PHE A 496 TRP 0.013 0.001 TRP A 544 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00379 (11874) covalent geometry : angle 0.57356 (16347) hydrogen bonds : bond 0.03329 ( 561) hydrogen bonds : angle 3.99796 ( 1543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 307 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8337 (ptmm) REVERT: A 507 MET cc_start: 0.9423 (ppp) cc_final: 0.8907 (ppp) REVERT: A 600 ASP cc_start: 0.9214 (t0) cc_final: 0.8823 (t0) REVERT: A 604 MET cc_start: 0.9370 (mmm) cc_final: 0.8730 (mmm) REVERT: A 908 ASP cc_start: 0.8471 (t0) cc_final: 0.8004 (t0) REVERT: A 956 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9061 (tm-30) REVERT: A 983 MET cc_start: 0.9405 (ttm) cc_final: 0.9073 (ttm) REVERT: A 1055 MET cc_start: 0.8768 (mpp) cc_final: 0.8506 (mpp) outliers start: 24 outliers final: 19 residues processed: 60 average time/residue: 0.0758 time to fit residues: 7.4313 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1307 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.0010 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.033869 restraints weight = 69732.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034929 restraints weight = 33203.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.035551 restraints weight = 22174.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035801 restraints weight = 17779.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036097 restraints weight = 15964.509| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11874 Z= 0.192 Angle : 0.577 11.098 16347 Z= 0.301 Chirality : 0.040 0.148 1816 Planarity : 0.003 0.043 1852 Dihedral : 18.446 151.109 2218 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 2.19 % Allowed : 21.90 % Favored : 75.91 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1219 helix: 1.94 (0.22), residues: 617 sheet: -0.76 (0.42), residues: 154 loop : 0.17 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1094 TYR 0.018 0.001 TYR A 61 PHE 0.035 0.001 PHE A 353 TRP 0.015 0.002 TRP A1085 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00417 (11874) covalent geometry : angle 0.57693 (16347) hydrogen bonds : bond 0.03402 ( 561) hydrogen bonds : angle 4.00181 ( 1543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.276 Fit side-chains REVERT: A 20 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 307 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8352 (ptmm) REVERT: A 507 MET cc_start: 0.9409 (ppp) cc_final: 0.9004 (ppp) REVERT: A 600 ASP cc_start: 0.9231 (t0) cc_final: 0.8855 (t0) REVERT: A 604 MET cc_start: 0.9349 (mmm) cc_final: 0.8520 (mmm) REVERT: A 908 ASP cc_start: 0.8448 (t0) cc_final: 0.7919 (t0) REVERT: A 956 GLN cc_start: 0.9590 (mm-40) cc_final: 0.9044 (tm-30) REVERT: A 1013 GLN cc_start: 0.9510 (mt0) cc_final: 0.9074 (mt0) REVERT: A 1055 MET cc_start: 0.8743 (mpp) cc_final: 0.8517 (mpp) REVERT: A 1306 ARG cc_start: 0.9427 (OUTLIER) cc_final: 0.9140 (mmt-90) outliers start: 24 outliers final: 20 residues processed: 61 average time/residue: 0.0748 time to fit residues: 7.2568 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034142 restraints weight = 69490.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035212 restraints weight = 33051.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035870 restraints weight = 21939.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036207 restraints weight = 17518.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.036401 restraints weight = 15719.259| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11874 Z= 0.176 Angle : 0.574 13.913 16347 Z= 0.296 Chirality : 0.040 0.158 1816 Planarity : 0.003 0.042 1852 Dihedral : 18.397 150.995 2218 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 20.62 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1219 helix: 1.99 (0.22), residues: 616 sheet: -0.69 (0.42), residues: 154 loop : 0.23 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.016 0.001 TYR A 61 PHE 0.043 0.001 PHE A 353 TRP 0.014 0.002 TRP A1085 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00384 (11874) covalent geometry : angle 0.57432 (16347) hydrogen bonds : bond 0.03230 ( 561) hydrogen bonds : angle 3.94758 ( 1543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8127 (tpt) cc_final: 0.7837 (tpt) REVERT: A 20 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 307 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8344 (ptmm) REVERT: A 507 MET cc_start: 0.9408 (ppp) cc_final: 0.8991 (ppp) REVERT: A 600 ASP cc_start: 0.9242 (t0) cc_final: 0.8844 (t0) REVERT: A 604 MET cc_start: 0.9367 (mmm) cc_final: 0.9106 (mmm) REVERT: A 908 ASP cc_start: 0.8425 (t0) cc_final: 0.7897 (t0) REVERT: A 956 GLN cc_start: 0.9565 (mm-40) cc_final: 0.9023 (tm-30) REVERT: A 1013 GLN cc_start: 0.9497 (mt0) cc_final: 0.9054 (mt0) REVERT: A 1055 MET cc_start: 0.8726 (mpp) cc_final: 0.8479 (mpt) REVERT: A 1275 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9103 (tp-100) REVERT: A 1290 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: A 1306 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9108 (mmt-90) outliers start: 32 outliers final: 22 residues processed: 70 average time/residue: 0.0914 time to fit residues: 9.9627 Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1275 GLN Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.050256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.033482 restraints weight = 71175.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.034532 restraints weight = 34061.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035151 restraints weight = 22735.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035501 restraints weight = 18266.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035679 restraints weight = 16230.916| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11874 Z= 0.218 Angle : 0.601 13.577 16347 Z= 0.313 Chirality : 0.041 0.212 1816 Planarity : 0.004 0.043 1852 Dihedral : 18.472 151.081 2218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 2.55 % Allowed : 21.26 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1219 helix: 1.98 (0.22), residues: 610 sheet: -0.80 (0.41), residues: 159 loop : 0.26 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1252 TYR 0.020 0.001 TYR A 61 PHE 0.041 0.002 PHE A 353 TRP 0.016 0.002 TRP A1085 HIS 0.006 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00470 (11874) covalent geometry : angle 0.60116 (16347) hydrogen bonds : bond 0.03563 ( 561) hydrogen bonds : angle 4.04624 ( 1543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 307 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8372 (ptmm) REVERT: A 507 MET cc_start: 0.9408 (ppp) cc_final: 0.9084 (ppp) REVERT: A 537 MET cc_start: 0.9086 (mmm) cc_final: 0.8834 (mmm) REVERT: A 600 ASP cc_start: 0.9284 (t0) cc_final: 0.8868 (t0) REVERT: A 604 MET cc_start: 0.9318 (mmm) cc_final: 0.9047 (mmm) REVERT: A 908 ASP cc_start: 0.8427 (t0) cc_final: 0.7895 (t0) REVERT: A 956 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9049 (tm-30) REVERT: A 1055 MET cc_start: 0.8736 (mpp) cc_final: 0.8487 (mpt) REVERT: A 1275 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.9116 (tp-100) REVERT: A 1290 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: A 1306 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.9160 (mmt-90) outliers start: 28 outliers final: 23 residues processed: 65 average time/residue: 0.1016 time to fit residues: 10.1793 Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1275 GLN Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 chunk 108 optimal weight: 0.0030 chunk 127 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.036006 restraints weight = 68700.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037120 restraints weight = 32876.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.037808 restraints weight = 21846.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038158 restraints weight = 17446.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038400 restraints weight = 15597.295| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11874 Z= 0.106 Angle : 0.569 13.940 16347 Z= 0.286 Chirality : 0.040 0.202 1816 Planarity : 0.003 0.040 1852 Dihedral : 18.235 149.457 2218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 1.64 % Allowed : 22.26 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.25), residues: 1219 helix: 2.12 (0.22), residues: 604 sheet: -0.51 (0.42), residues: 154 loop : 0.31 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 947 TYR 0.013 0.001 TYR A 47 PHE 0.040 0.001 PHE A 353 TRP 0.013 0.001 TRP A1085 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00232 (11874) covalent geometry : angle 0.56881 (16347) hydrogen bonds : bond 0.02904 ( 561) hydrogen bonds : angle 3.77834 ( 1543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.38 seconds wall clock time: 33 minutes 12.39 seconds (1992.39 seconds total)