Starting phenix.real_space_refine on Fri Jul 3 01:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_40442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_40442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_40442.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_40442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2026/8sfi_40442.cif" } 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-dev-6108/lib/python3.11/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: 2.75, per 1000 atoms: 0.24 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: 0.79 Conformation dependent library (CDL) restraints added in 499.0 milliseconds 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: 1.32 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: 2.58 Time building geometry restraints manager: 1.08 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=" C3' DG D 15 " pdb=" C2' DG D 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.39e+00 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=" C3' DT D 16 " pdb=" C2' DT D 16 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.75e+00 bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.55e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 15957 2.71 - 5.42: 258 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=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sigma weight residual 117.70 124.54 -6.84 1.20e+00 6.94e-01 3.25e+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 ... (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: 1690 0.104 - 0.208: 105 0.208 - 0.311: 4 0.311 - 0.415: 11 0.415 - 0.519: 6 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 2.34 -2.77 -0.44 2.00e-01 2.50e+01 4.76e+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 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.61e+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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.870 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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= 0.294 Angle : 1.097 13.549 16347 Z= 0.609 Chirality : 0.064 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 are 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/Z covalent geometry : bond 0.00523 / 0.29 (11874) covalent geometry : angle 1.09665 / 0.61 (16347) hydrogen bonds : bond 0.13099 / 8.99 ( 561) hydrogen bonds : angle 5.87020 / 4.17 ( 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 : 0.254 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: 0.0921 time to fit residues: 13.8657 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 : 0.504 ------------------------------------------------------------------------------- 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: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 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... ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** 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 = 0.3361 r_free = 0.3361 target = 0.055771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039003 restraints weight = 65625.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.040185 restraints weight = 30941.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.040938 restraints weight = 20402.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041320 restraints weight = 15971.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.041546 restraints weight = 13956.564| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11874 Z= 0.133 Angle : 0.639 9.038 16347 Z= 0.336 Chirality : 0.043 0.248 1816 Planarity : 0.005 0.074 1852 Dihedral : 18.441 151.366 2219 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 22.17 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1219 helix: 0.61 (0.21), residues: 604 sheet: -0.89 (0.42), residues: 150 loop : -0.50 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.016 0.001 TYR A 173 PHE 0.029 0.001 PHE A 496 TRP 0.012 0.001 TRP A1085 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11874) covalent geometry : angle 0.63864 / 0.34 (16347) hydrogen bonds : bond 0.04103 / 2.75 ( 561) hydrogen bonds : angle 4.63636 / 3.25 ( 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 86 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7558 (tpt) cc_final: 0.7163 (tpt) REVERT: A 507 MET cc_start: 0.9349 (ppp) cc_final: 0.9055 (ppp) REVERT: A 600 ASP cc_start: 0.8442 (t0) cc_final: 0.8058 (t0) REVERT: A 604 MET cc_start: 0.9225 (mmm) cc_final: 0.8997 (mmm) REVERT: A 619 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9194 (m-80) REVERT: A 908 ASP cc_start: 0.7804 (t0) cc_final: 0.7370 (t0) REVERT: A 1017 LYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9267 (tptm) REVERT: A 1260 MET cc_start: 0.8930 (mmt) cc_final: 0.8684 (mmm) outliers start: 22 outliers final: 7 residues processed: 82 average time/residue: 0.0874 time to fit residues: 11.2011 Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 368 HIS 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 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: 20.0000 chunk 54 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 224 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.051470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.034705 restraints weight = 69647.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035780 restraints weight = 33582.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036420 restraints weight = 22369.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036775 restraints weight = 18002.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.036978 restraints weight = 16042.972| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 11874 Z= 0.351 Angle : 0.749 8.258 16347 Z= 0.401 Chirality : 0.045 0.220 1816 Planarity : 0.005 0.064 1852 Dihedral : 18.532 151.825 2218 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 3.83 % Allowed : 19.98 % 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 are not related in a simple way. whole: 0.48 (0.24), residues: 1219 helix: 1.12 (0.21), residues: 616 sheet: -1.12 (0.40), residues: 157 loop : -0.09 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 84 TYR 0.018 0.002 TYR A1069 PHE 0.029 0.002 PHE A 938 TRP 0.016 0.002 TRP A 544 HIS 0.012 0.001 HIS A 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.35 (11874) covalent geometry : angle 0.74857 / 0.40 (16347) hydrogen bonds : bond 0.05276 / 3.44 ( 561) hydrogen bonds : angle 4.59434 / 3.25 ( 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 88 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 46 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 507 MET cc_start: 0.9384 (ppp) cc_final: 0.9155 (ppp) REVERT: A 600 ASP cc_start: 0.9009 (t0) cc_final: 0.8578 (t0) REVERT: A 604 MET cc_start: 0.9367 (mmm) cc_final: 0.9111 (mmm) REVERT: A 651 GLU cc_start: 0.9159 (mp0) cc_final: 0.8892 (mp0) REVERT: A 908 ASP cc_start: 0.8180 (t0) cc_final: 0.7763 (t0) REVERT: A 992 LEU cc_start: 0.9598 (mt) cc_final: 0.9391 (mm) REVERT: A 1013 GLN cc_start: 0.9510 (mt0) cc_final: 0.9186 (mt0) REVERT: A 1017 LYS cc_start: 0.9541 (tptm) cc_final: 0.9291 (tptm) REVERT: A 1018 MET cc_start: 0.9585 (mtm) cc_final: 0.9173 (mtm) outliers start: 42 outliers final: 26 residues processed: 85 average time/residue: 0.0833 time to fit residues: 10.7930 Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 69 VAL 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 189 ILE Chi-restraints excluded: chain A residue 205 CYS 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 526 TYR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 984 ILE 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 1192 VAL Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.052997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036056 restraints weight = 67548.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037164 restraints weight = 32796.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037803 restraints weight = 21869.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038165 restraints weight = 17522.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038284 restraints weight = 15643.298| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11874 Z= 0.145 Angle : 0.557 7.265 16347 Z= 0.302 Chirality : 0.041 0.194 1816 Planarity : 0.004 0.055 1852 Dihedral : 18.584 151.004 2218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 2.74 % Allowed : 20.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1219 helix: 1.47 (0.21), residues: 610 sheet: -0.88 (0.41), residues: 154 loop : -0.01 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 947 TYR 0.016 0.001 TYR A 61 PHE 0.019 0.001 PHE A 938 TRP 0.014 0.002 TRP A1085 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11874) covalent geometry : angle 0.55714 / 0.30 (16347) hydrogen bonds : bond 0.03628 / 2.35 ( 561) hydrogen bonds : angle 4.19457 / 2.95 ( 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: 30 poor density : 46 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7941 (tpt) cc_final: 0.7590 (tpt) REVERT: A 20 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 51 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9124 (tttt) REVERT: A 507 MET cc_start: 0.9419 (ppp) cc_final: 0.9035 (ppp) REVERT: A 600 ASP cc_start: 0.8912 (t0) cc_final: 0.8501 (t0) REVERT: A 604 MET cc_start: 0.9381 (mmm) cc_final: 0.9136 (mmm) REVERT: A 651 GLU cc_start: 0.9099 (mp0) cc_final: 0.8840 (mp0) REVERT: A 908 ASP cc_start: 0.8123 (t0) cc_final: 0.7699 (t0) REVERT: A 992 LEU cc_start: 0.9561 (mt) cc_final: 0.9350 (mm) REVERT: A 1013 GLN cc_start: 0.9478 (mt0) cc_final: 0.9145 (mt0) REVERT: A 1017 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9290 (tptm) outliers start: 30 outliers final: 21 residues processed: 71 average time/residue: 0.0902 time to fit residues: 9.9611 Evaluate side-chains 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 181 SER 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 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 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 984 ILE 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 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS 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: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3239 r_free = 0.3239 target = 0.050774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033852 restraints weight = 70239.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.034910 restraints weight = 34344.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035542 restraints weight = 23076.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035861 restraints weight = 18609.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036053 restraints weight = 16510.109| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11874 Z= 0.307 Angle : 0.667 7.497 16347 Z= 0.358 Chirality : 0.044 0.215 1816 Planarity : 0.004 0.056 1852 Dihedral : 18.662 152.858 2218 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 4.38 % Allowed : 18.43 % Favored : 77.19 % 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 are not related in a simple way. whole: 0.81 (0.25), residues: 1219 helix: 1.48 (0.21), residues: 623 sheet: -1.14 (0.40), residues: 159 loop : -0.02 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 681 TYR 0.021 0.002 TYR A 61 PHE 0.019 0.002 PHE A 201 TRP 0.017 0.002 TRP A 544 HIS 0.007 0.001 HIS A 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.31 (11874) covalent geometry : angle 0.66694 / 0.36 (16347) hydrogen bonds : bond 0.04551 / 2.94 ( 561) hydrogen bonds : angle 4.37375 / 3.10 ( 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 91 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 43 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 51 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9157 (tttt) REVERT: A 507 MET cc_start: 0.9435 (ppp) cc_final: 0.9026 (ppp) REVERT: A 600 ASP cc_start: 0.9150 (t0) cc_final: 0.8753 (t0) REVERT: A 604 MET cc_start: 0.9326 (mmm) cc_final: 0.9063 (mmm) REVERT: A 651 GLU cc_start: 0.9150 (mp0) cc_final: 0.8911 (mp0) REVERT: A 908 ASP cc_start: 0.8351 (t0) cc_final: 0.7896 (t0) REVERT: A 1013 GLN cc_start: 0.9524 (mt0) cc_final: 0.9213 (mt0) REVERT: A 1017 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9300 (tptm) REVERT: A 1243 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8533 (p0) REVERT: A 1290 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7949 (tp40) outliers start: 48 outliers final: 26 residues processed: 87 average time/residue: 0.0941 time to fit residues: 12.7267 Evaluate side-chains 72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 234 SER 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 568 MET Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL 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 1058 GLN 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 1243 ASP Chi-restraints excluded: chain A residue 1290 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.052057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.035041 restraints weight = 69220.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.036131 restraints weight = 33085.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.036811 restraints weight = 22183.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037207 restraints weight = 17659.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037364 restraints weight = 15572.220| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3178 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 : 0.557 12.488 16347 Z= 0.297 Chirality : 0.041 0.192 1816 Planarity : 0.003 0.050 1852 Dihedral : 18.615 152.185 2218 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 3.28 % Allowed : 19.62 % 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 are not related in a simple way. whole: 1.10 (0.25), residues: 1219 helix: 1.70 (0.22), residues: 616 sheet: -0.88 (0.41), residues: 154 loop : 0.09 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1306 TYR 0.018 0.001 TYR A 61 PHE 0.017 0.001 PHE A 496 TRP 0.015 0.002 TRP A1085 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11874) covalent geometry : angle 0.55660 / 0.30 (16347) hydrogen bonds : bond 0.03498 / 2.24 ( 561) hydrogen bonds : angle 4.04080 / 2.85 ( 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 79 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 43 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 159 LEU cc_start: 0.9803 (tt) cc_final: 0.9389 (pp) REVERT: A 507 MET cc_start: 0.9439 (ppp) cc_final: 0.8982 (ppp) REVERT: A 600 ASP cc_start: 0.9061 (t0) cc_final: 0.8625 (t0) REVERT: A 604 MET cc_start: 0.9343 (mmm) cc_final: 0.9121 (mmm) REVERT: A 651 GLU cc_start: 0.9137 (mp0) cc_final: 0.8909 (mp0) REVERT: A 908 ASP cc_start: 0.8376 (t0) cc_final: 0.7940 (t0) REVERT: A 1017 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9220 (tptm) REVERT: A 1243 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8435 (p0) REVERT: A 1290 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7629 (mp10) outliers start: 36 outliers final: 24 residues processed: 74 average time/residue: 0.0941 time to fit residues: 10.5572 Evaluate side-chains 70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 447 HIS Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU 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 1017 LYS Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 GLN 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 1243 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1290 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.034407 restraints weight = 70210.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035474 restraints weight = 33837.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.036119 restraints weight = 22633.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036473 restraints weight = 18156.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036674 restraints weight = 16079.153| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11874 Z= 0.211 Angle : 0.574 10.835 16347 Z= 0.308 Chirality : 0.041 0.200 1816 Planarity : 0.004 0.050 1852 Dihedral : 18.578 152.750 2218 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 2.74 % Allowed : 19.89 % Favored : 77.37 % 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 are not related in a simple way. whole: 1.11 (0.25), residues: 1219 helix: 1.68 (0.22), residues: 623 sheet: -0.94 (0.41), residues: 154 loop : 0.15 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1306 TYR 0.017 0.001 TYR A 61 PHE 0.020 0.001 PHE A 496 TRP 0.012 0.002 TRP A 544 HIS 0.011 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (11874) covalent geometry : angle 0.57444 / 0.31 (16347) hydrogen bonds : bond 0.03697 / 2.36 ( 561) hydrogen bonds : angle 4.08113 / 2.88 ( 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 72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 159 LEU cc_start: 0.9826 (tt) cc_final: 0.9426 (pp) REVERT: A 507 MET cc_start: 0.9456 (ppp) cc_final: 0.8978 (ppp) REVERT: A 600 ASP cc_start: 0.9118 (t0) cc_final: 0.8714 (t0) REVERT: A 604 MET cc_start: 0.9346 (mmm) cc_final: 0.9133 (mmm) REVERT: A 651 GLU cc_start: 0.9170 (mp0) cc_final: 0.8945 (mp0) REVERT: A 908 ASP cc_start: 0.8401 (t0) cc_final: 0.7945 (t0) REVERT: A 1013 GLN cc_start: 0.9504 (mt0) cc_final: 0.9069 (mt0) REVERT: A 1017 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9237 (tptm) REVERT: A 1018 MET cc_start: 0.9485 (mtm) cc_final: 0.9155 (mtm) REVERT: A 1243 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8474 (p0) REVERT: A 1290 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7739 (mp10) outliers start: 30 outliers final: 23 residues processed: 68 average time/residue: 0.0938 time to fit residues: 10.2251 Evaluate side-chains 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 754 HIS Chi-restraints excluded: chain A residue 763 LEU 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 1017 LYS Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 GLN 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 1243 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1290 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 0.0060 chunk 60 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.051845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034896 restraints weight = 69231.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.035990 restraints weight = 33384.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036602 restraints weight = 22260.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036966 restraints weight = 17822.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037086 restraints weight = 15908.563| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11874 Z= 0.148 Angle : 0.541 10.261 16347 Z= 0.289 Chirality : 0.040 0.190 1816 Planarity : 0.003 0.049 1852 Dihedral : 18.534 152.542 2218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 20.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1219 helix: 1.83 (0.22), residues: 623 sheet: -0.78 (0.41), residues: 152 loop : 0.18 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1306 TYR 0.015 0.001 TYR A 61 PHE 0.022 0.001 PHE A 496 TRP 0.015 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (11874) covalent geometry : angle 0.54113 / 0.29 (16347) hydrogen bonds : bond 0.03315 / 2.12 ( 561) hydrogen bonds : angle 3.92555 / 2.76 ( 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 75 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 159 LEU cc_start: 0.9819 (tt) cc_final: 0.9425 (pp) REVERT: A 307 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8426 (ptmm) REVERT: A 353 PHE cc_start: 0.9128 (m-10) cc_final: 0.8881 (m-80) REVERT: A 507 MET cc_start: 0.9449 (ppp) cc_final: 0.8954 (ppp) REVERT: A 544 TRP cc_start: 0.9328 (OUTLIER) cc_final: 0.8504 (m100) REVERT: A 600 ASP cc_start: 0.9086 (t0) cc_final: 0.8661 (t0) REVERT: A 651 GLU cc_start: 0.9160 (mp0) cc_final: 0.8941 (mp0) REVERT: A 908 ASP cc_start: 0.8416 (t0) cc_final: 0.7943 (t0) REVERT: A 1017 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9207 (tptm) REVERT: A 1018 MET cc_start: 0.9494 (mtm) cc_final: 0.9166 (mtm) REVERT: A 1243 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8421 (p0) REVERT: A 1290 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7797 (mp10) outliers start: 30 outliers final: 21 residues processed: 71 average time/residue: 0.0986 time to fit residues: 11.0010 Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU 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 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 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1290 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 112 optimal weight: 0.0270 chunk 66 optimal weight: 0.4980 chunk 92 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035206 restraints weight = 68267.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036287 restraints weight = 32583.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036927 restraints weight = 21646.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037291 restraints weight = 17305.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.037494 restraints weight = 15284.089| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11874 Z= 0.143 Angle : 0.536 9.776 16347 Z= 0.284 Chirality : 0.040 0.184 1816 Planarity : 0.003 0.047 1852 Dihedral : 18.457 152.435 2218 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 2.65 % Allowed : 20.71 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1219 helix: 1.97 (0.22), residues: 620 sheet: -0.76 (0.41), residues: 152 loop : 0.29 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1306 TYR 0.014 0.001 TYR A 61 PHE 0.026 0.001 PHE A 496 TRP 0.014 0.001 TRP A1085 HIS 0.003 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11874) covalent geometry : angle 0.53566 / 0.28 (16347) hydrogen bonds : bond 0.03251 / 2.10 ( 561) hydrogen bonds : angle 3.86527 / 2.71 ( 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 74 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 159 LEU cc_start: 0.9824 (tt) cc_final: 0.9443 (pp) REVERT: A 307 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8363 (ptmm) REVERT: A 353 PHE cc_start: 0.9127 (m-10) cc_final: 0.8867 (m-80) REVERT: A 507 MET cc_start: 0.9456 (ppp) cc_final: 0.8940 (ppp) REVERT: A 544 TRP cc_start: 0.9309 (OUTLIER) cc_final: 0.8514 (m100) REVERT: A 600 ASP cc_start: 0.9031 (t0) cc_final: 0.8595 (t0) REVERT: A 651 GLU cc_start: 0.9161 (mp0) cc_final: 0.8949 (mp0) REVERT: A 908 ASP cc_start: 0.8414 (t0) cc_final: 0.7940 (t0) REVERT: A 1018 MET cc_start: 0.9512 (mtm) cc_final: 0.9195 (mtm) REVERT: A 1243 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8414 (p0) REVERT: A 1290 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7911 (mp10) outliers start: 29 outliers final: 21 residues processed: 71 average time/residue: 0.1006 time to fit residues: 11.0532 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 : 0.432 ------------------------------------------------------------------------------- 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 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 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU 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 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 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3220 r_free = 0.3220 target = 0.049928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033160 restraints weight = 71941.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.034172 restraints weight = 34697.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.034778 restraints weight = 23407.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035017 restraints weight = 18833.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.035264 restraints weight = 17149.436| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11874 Z= 0.358 Angle : 0.714 15.055 16347 Z= 0.375 Chirality : 0.044 0.225 1816 Planarity : 0.004 0.072 1852 Dihedral : 18.636 153.322 2218 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 2.37 % Allowed : 21.44 % 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 are not related in a simple way. whole: 1.05 (0.25), residues: 1219 helix: 1.63 (0.21), residues: 622 sheet: -1.10 (0.40), residues: 157 loop : 0.20 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 951 TYR 0.024 0.002 TYR A 61 PHE 0.023 0.002 PHE A 496 TRP 0.019 0.002 TRP A 544 HIS 0.008 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.36 (11874) covalent geometry : angle 0.71359 / 0.37 (16347) hydrogen bonds : bond 0.04621 / 2.97 ( 561) hydrogen bonds : angle 4.31136 / 3.05 ( 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.382 Fit side-chains REVERT: A 20 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 507 MET cc_start: 0.9437 (ppp) cc_final: 0.8933 (ppp) REVERT: A 544 TRP cc_start: 0.9458 (OUTLIER) cc_final: 0.8707 (m100) REVERT: A 600 ASP cc_start: 0.9261 (t0) cc_final: 0.8897 (t0) REVERT: A 651 GLU cc_start: 0.9178 (mp0) cc_final: 0.8955 (mp0) REVERT: A 908 ASP cc_start: 0.8474 (t0) cc_final: 0.7964 (t0) REVERT: A 956 GLN cc_start: 0.9559 (mm-40) cc_final: 0.8994 (tm-30) REVERT: A 1013 GLN cc_start: 0.9531 (mt0) cc_final: 0.9092 (mt0) REVERT: A 1017 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9254 (tptm) REVERT: A 1243 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8579 (p0) outliers start: 26 outliers final: 22 residues processed: 63 average time/residue: 0.0947 time to fit residues: 9.5777 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU 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 1017 LYS Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 GLN 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 1243 ASP Chi-restraints excluded: chain A residue 1290 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3257 r_free = 0.3257 target = 0.051431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.034468 restraints weight = 69271.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035539 restraints weight = 33198.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036166 restraints weight = 22199.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036524 restraints weight = 17770.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.036648 restraints weight = 15858.459| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11874 Z= 0.142 Angle : 0.575 12.795 16347 Z= 0.303 Chirality : 0.041 0.196 1816 Planarity : 0.003 0.045 1852 Dihedral : 18.599 152.779 2218 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 2.46 % Allowed : 21.53 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1219 helix: 1.81 (0.22), residues: 625 sheet: -0.85 (0.41), residues: 154 loop : 0.32 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 951 TYR 0.016 0.001 TYR A 61 PHE 0.017 0.001 PHE A 496 TRP 0.019 0.002 TRP A1085 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11874) covalent geometry : angle 0.57503 / 0.30 (16347) hydrogen bonds : bond 0.03404 / 2.19 ( 561) hydrogen bonds : angle 3.97607 / 2.78 ( 1543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.75 seconds wall clock time: 35 minutes 24.99 seconds (2124.99 seconds total)