Starting phenix.real_space_refine on Tue Jul 29 14:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfi_40442/07_2025/8sfi_40442.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.54, per 1000 atoms: 0.66 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: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.22 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: 5.99 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2956 1.34 - 1.46: 2772 1.46 - 1.58: 5970 1.58 - 1.70: 138 1.70 - 1.82: 38 Bond restraints: 11874 Sorted by residual: bond pdb=" CB PRO A 648 " pdb=" CG PRO A 648 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " ideal model delta sigma weight residual 1.520 1.601 -0.081 3.00e-02 1.11e+03 7.24e+00 bond pdb=" CB LYS A 965 " pdb=" CG LYS A 965 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ARG A 411 " pdb=" CG ARG A 411 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.24e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 15964 2.71 - 5.42: 251 5.42 - 8.13: 64 8.13 - 10.84: 55 10.84 - 13.55: 13 Bond angle restraints: 16347 Sorted by residual: angle pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" CD PRO A 648 " ideal model delta sigma weight residual 112.00 98.45 13.55 1.40e+00 5.10e-01 9.37e+01 angle pdb=" N ASP A 939 " pdb=" CA ASP A 939 " pdb=" C ASP A 939 " ideal model delta sigma weight residual 110.24 118.36 -8.12 1.30e+00 5.92e-01 3.90e+01 angle pdb=" CB LYS A 468 " pdb=" CG LYS A 468 " pdb=" CD LYS A 468 " ideal model delta sigma weight residual 111.30 123.87 -12.57 2.30e+00 1.89e-01 2.99e+01 angle pdb=" C PHE A 938 " pdb=" CA PHE A 938 " pdb=" CB PHE A 938 " ideal model delta sigma weight residual 111.74 120.37 -8.63 1.59e+00 3.96e-01 2.95e+01 angle pdb=" CA LYS A1109 " pdb=" CB LYS A1109 " pdb=" CG LYS A1109 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 ... (remaining 16342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 6491 30.65 - 61.29: 550 61.29 - 91.94: 38 91.94 - 122.58: 0 122.58 - 153.23: 2 Dihedral angle restraints: 7081 sinusoidal: 3463 harmonic: 3618 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 46.77 153.23 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 53.50 146.50 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" CA THR A 522 " pdb=" C THR A 522 " pdb=" N LYS A 523 " pdb=" CA LYS A 523 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 7078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1695 0.104 - 0.208: 100 0.208 - 0.311: 6 0.311 - 0.415: 11 0.415 - 0.519: 4 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CG LEU A 471 " pdb=" CB LEU A 471 " pdb=" CD1 LEU A 471 " pdb=" CD2 LEU A 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1813 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A 606 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 537 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 538 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 647 " -0.065 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 648 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.049 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1305 2.75 - 3.29: 11003 3.29 - 3.83: 20297 3.83 - 4.36: 23053 4.36 - 4.90: 38033 Nonbonded interactions: 93691 Sorted by model distance: nonbonded pdb=" O GLU A 441 " pdb=" OG SER A 444 " model vdw 2.218 3.040 nonbonded pdb=" O ASN A1090 " pdb=" OG SER A1093 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 11 " pdb=" OD1 ASN A1024 " model vdw 2.290 3.040 nonbonded pdb=" O GLN A 437 " pdb=" OG SER A 440 " model vdw 2.299 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.300 3.040 ... (remaining 93686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 270.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 309.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 11874 Z= 0.213 Angle : 1.079 13.549 16347 Z= 0.527 Chirality : 0.063 0.519 1816 Planarity : 0.008 0.132 1852 Dihedral : 19.823 153.226 4739 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.46 % Allowed : 24.27 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.028 0.002 TRP A1085 HIS 0.006 0.001 HIS A 445 PHE 0.049 0.003 PHE A1117 TYR 0.030 0.002 TYR A 746 ARG 0.012 0.001 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.13099 ( 561) hydrogen bonds : angle 5.87020 ( 1543) covalent geometry : bond 0.00490 (11874) covalent geometry : angle 1.07862 (16347) *********************** 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 : 1.224 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: 0.2314 time to fit residues: 35.0288 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 : 1.283 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0070 chunk 97 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3326 r_free = 0.3326 target = 0.054199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037226 restraints weight = 67927.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038343 restraints weight = 32334.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039003 restraints weight = 21644.238| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11874 Z= 0.155 Angle : 0.599 8.486 16347 Z= 0.313 Chirality : 0.041 0.247 1816 Planarity : 0.005 0.071 1852 Dihedral : 18.233 149.463 2219 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.65 % Allowed : 20.99 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1219 helix: 1.04 (0.21), residues: 607 sheet: -0.91 (0.42), residues: 152 loop : -0.25 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A 447 PHE 0.020 0.001 PHE A 496 TYR 0.013 0.001 TYR A 61 ARG 0.004 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 561) hydrogen bonds : angle 4.30870 ( 1543) covalent geometry : bond 0.00341 (11874) covalent geometry : angle 0.59903 (16347) *********************** 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 87 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 600 ASP cc_start: 0.8576 (t0) cc_final: 0.8171 (t0) REVERT: A 604 MET cc_start: 0.9251 (mmm) cc_final: 0.9026 (mmm) REVERT: A 908 ASP cc_start: 0.8139 (t0) cc_final: 0.7813 (t0) REVERT: A 1013 GLN cc_start: 0.9486 (mt0) cc_final: 0.9166 (mt0) REVERT: A 1018 MET cc_start: 0.9461 (mtm) cc_final: 0.8992 (mtm) REVERT: A 1260 MET cc_start: 0.9040 (mmt) cc_final: 0.8800 (mmm) outliers start: 29 outliers final: 12 residues processed: 84 average time/residue: 0.2531 time to fit residues: 32.8938 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033635 restraints weight = 70571.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.034705 restraints weight = 33531.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035308 restraints weight = 22361.476| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11874 Z= 0.299 Angle : 0.661 8.976 16347 Z= 0.354 Chirality : 0.043 0.163 1816 Planarity : 0.004 0.055 1852 Dihedral : 18.672 151.956 2219 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 4.11 % Allowed : 19.62 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1219 helix: 1.36 (0.21), residues: 623 sheet: -0.93 (0.42), residues: 154 loop : 0.04 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 544 HIS 0.007 0.001 HIS A1269 PHE 0.017 0.002 PHE A 201 TYR 0.020 0.002 TYR A 61 ARG 0.004 0.001 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 561) hydrogen bonds : angle 4.38920 ( 1543) covalent geometry : bond 0.00635 (11874) covalent geometry : angle 0.66113 (16347) *********************** 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 89 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 44 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 51 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9004 (ttmt) REVERT: A 600 ASP cc_start: 0.9222 (t0) cc_final: 0.8851 (t0) REVERT: A 604 MET cc_start: 0.9283 (mmm) cc_final: 0.9081 (mmm) REVERT: A 908 ASP cc_start: 0.8366 (t0) cc_final: 0.7871 (t0) REVERT: A 1013 GLN cc_start: 0.9525 (mt0) cc_final: 0.9207 (mt0) REVERT: A 1017 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9298 (tptm) REVERT: A 1055 MET cc_start: 0.9147 (mtm) cc_final: 0.8848 (mpp) REVERT: A 1225 MET cc_start: 0.8907 (mmm) cc_final: 0.8549 (mmm) REVERT: A 1306 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.9027 (mtt-85) outliers start: 45 outliers final: 24 residues processed: 84 average time/residue: 0.2810 time to fit residues: 36.1257 Evaluate side-chains 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 27 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3252 r_free = 0.3252 target = 0.051248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.034197 restraints weight = 69603.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035233 restraints weight = 33771.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035849 restraints weight = 22751.501| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11874 Z= 0.201 Angle : 0.591 13.920 16347 Z= 0.306 Chirality : 0.040 0.152 1816 Planarity : 0.004 0.047 1852 Dihedral : 18.553 152.136 2219 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 2.92 % Allowed : 20.53 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1219 helix: 1.67 (0.22), residues: 619 sheet: -0.86 (0.41), residues: 154 loop : 0.07 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.018 0.001 PHE A 496 TYR 0.016 0.001 TYR A 61 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 561) hydrogen bonds : angle 4.10757 ( 1543) covalent geometry : bond 0.00432 (11874) covalent geometry : angle 0.59149 (16347) *********************** 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 72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 307 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8502 (ptmm) REVERT: A 600 ASP cc_start: 0.9120 (t0) cc_final: 0.8771 (t0) REVERT: A 908 ASP cc_start: 0.8477 (t0) cc_final: 0.7938 (t0) REVERT: A 1017 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9281 (tptm) REVERT: A 1289 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8961 (mm) outliers start: 32 outliers final: 21 residues processed: 67 average time/residue: 0.3838 time to fit residues: 41.2424 Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 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 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.034348 restraints weight = 69236.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035424 restraints weight = 33379.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.036058 restraints weight = 22358.119| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11874 Z= 0.171 Angle : 0.555 12.161 16347 Z= 0.288 Chirality : 0.040 0.153 1816 Planarity : 0.003 0.044 1852 Dihedral : 18.462 151.257 2219 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 3.47 % Allowed : 20.44 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1219 helix: 1.82 (0.22), residues: 623 sheet: -0.78 (0.41), residues: 154 loop : 0.08 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.012 0.001 PHE A 496 TYR 0.015 0.001 TYR A 61 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 561) hydrogen bonds : angle 3.92836 ( 1543) covalent geometry : bond 0.00373 (11874) covalent geometry : angle 0.55516 (16347) *********************** 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 81 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 43 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 307 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: A 353 PHE cc_start: 0.9161 (m-80) cc_final: 0.8943 (m-80) REVERT: A 600 ASP cc_start: 0.9125 (t0) cc_final: 0.8750 (t0) REVERT: A 908 ASP cc_start: 0.8466 (t0) cc_final: 0.7909 (t0) REVERT: A 983 MET cc_start: 0.9316 (ttm) cc_final: 0.9023 (ttm) REVERT: A 1013 GLN cc_start: 0.9504 (mt0) cc_final: 0.9126 (mt0) REVERT: A 1017 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9248 (tptm) REVERT: A 1055 MET cc_start: 0.9046 (mtm) cc_final: 0.8812 (mpp) REVERT: A 1289 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8899 (mm) outliers start: 38 outliers final: 22 residues processed: 76 average time/residue: 0.4346 time to fit residues: 48.3476 Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 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 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 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 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 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3257 r_free = 0.3257 target = 0.051465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.034638 restraints weight = 70200.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.035720 restraints weight = 33324.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036340 restraints weight = 22260.869| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11874 Z= 0.156 Angle : 0.558 13.167 16347 Z= 0.287 Chirality : 0.039 0.151 1816 Planarity : 0.003 0.042 1852 Dihedral : 18.385 150.622 2219 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 2.74 % Allowed : 20.99 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1219 helix: 1.96 (0.22), residues: 621 sheet: -0.70 (0.42), residues: 154 loop : 0.20 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.021 0.001 PHE A 496 TYR 0.014 0.001 TYR A 61 ARG 0.007 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 561) hydrogen bonds : angle 3.89019 ( 1543) covalent geometry : bond 0.00343 (11874) covalent geometry : angle 0.55803 (16347) *********************** 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 74 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 159 LEU cc_start: 0.9773 (tt) cc_final: 0.9332 (pp) REVERT: A 307 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8353 (ptmm) REVERT: A 353 PHE cc_start: 0.9182 (m-10) cc_final: 0.8952 (m-80) REVERT: A 507 MET cc_start: 0.9321 (ppp) cc_final: 0.8832 (ppp) REVERT: A 544 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.8560 (m100) REVERT: A 600 ASP cc_start: 0.9139 (t0) cc_final: 0.8756 (t0) REVERT: A 604 MET cc_start: 0.9413 (mmm) cc_final: 0.8763 (mmm) REVERT: A 786 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8348 (mt-10) REVERT: A 908 ASP cc_start: 0.8464 (t0) cc_final: 0.7878 (t0) REVERT: A 956 GLN cc_start: 0.9608 (mm-40) cc_final: 0.9036 (tm-30) REVERT: A 1013 GLN cc_start: 0.9497 (mt0) cc_final: 0.9116 (mt0) REVERT: A 1017 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9242 (tptm) REVERT: A 1289 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8924 (mm) REVERT: A 1306 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.8870 (mmt-90) outliers start: 30 outliers final: 22 residues processed: 71 average time/residue: 0.3476 time to fit residues: 37.1558 Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 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 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 1017 LYS 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 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3248 r_free = 0.3248 target = 0.051002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.034218 restraints weight = 71198.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.035317 restraints weight = 33620.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035929 restraints weight = 22242.528| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11874 Z= 0.179 Angle : 0.573 13.442 16347 Z= 0.296 Chirality : 0.039 0.156 1816 Planarity : 0.003 0.043 1852 Dihedral : 18.375 150.166 2219 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.56 % Allowed : 20.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1219 helix: 1.96 (0.22), residues: 623 sheet: -0.69 (0.42), residues: 154 loop : 0.15 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.010 0.001 PHE A 496 TYR 0.016 0.001 TYR A 61 ARG 0.004 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 561) hydrogen bonds : angle 3.87169 ( 1543) covalent geometry : bond 0.00391 (11874) covalent geometry : angle 0.57348 (16347) *********************** 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 80 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 41 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 307 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8366 (ptmm) REVERT: A 353 PHE cc_start: 0.9194 (m-10) cc_final: 0.8977 (m-80) REVERT: A 507 MET cc_start: 0.9330 (ppp) cc_final: 0.8881 (ppp) REVERT: A 544 TRP cc_start: 0.9333 (OUTLIER) cc_final: 0.8554 (m100) REVERT: A 600 ASP cc_start: 0.9220 (t0) cc_final: 0.8849 (t0) REVERT: A 604 MET cc_start: 0.9406 (mmm) cc_final: 0.8772 (mmm) REVERT: A 908 ASP cc_start: 0.8478 (t0) cc_final: 0.7912 (t0) REVERT: A 956 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9006 (tm-30) REVERT: A 983 MET cc_start: 0.9309 (ttm) cc_final: 0.9046 (ttm) REVERT: A 1013 GLN cc_start: 0.9512 (mt0) cc_final: 0.9062 (mt0) REVERT: A 1017 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9246 (tptm) REVERT: A 1289 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 1306 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8759 (mmt-90) outliers start: 39 outliers final: 23 residues processed: 77 average time/residue: 0.3898 time to fit residues: 45.1985 Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 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 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 1017 LYS 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 1278 LEU Chi-restraints excluded: chain A residue 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3240 r_free = 0.3240 target = 0.050592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.033782 restraints weight = 70436.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034829 restraints weight = 33539.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.035449 restraints weight = 22436.526| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11874 Z= 0.202 Angle : 0.588 13.400 16347 Z= 0.305 Chirality : 0.040 0.204 1816 Planarity : 0.003 0.042 1852 Dihedral : 18.415 150.484 2219 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 3.01 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1219 helix: 2.10 (0.22), residues: 610 sheet: -0.75 (0.42), residues: 154 loop : 0.15 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1085 HIS 0.005 0.001 HIS A1269 PHE 0.011 0.001 PHE A 496 TYR 0.018 0.001 TYR A 61 ARG 0.004 0.000 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 561) hydrogen bonds : angle 3.92885 ( 1543) covalent geometry : bond 0.00438 (11874) covalent geometry : angle 0.58828 (16347) *********************** 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 76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 43 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 307 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8346 (ptmm) REVERT: A 353 PHE cc_start: 0.9206 (m-10) cc_final: 0.8991 (m-80) REVERT: A 507 MET cc_start: 0.9360 (ppp) cc_final: 0.8951 (ppp) REVERT: A 544 TRP cc_start: 0.9368 (OUTLIER) cc_final: 0.8716 (m100) REVERT: A 600 ASP cc_start: 0.9260 (t0) cc_final: 0.8917 (t0) REVERT: A 604 MET cc_start: 0.9356 (mmm) cc_final: 0.8520 (mmm) REVERT: A 908 ASP cc_start: 0.8476 (t0) cc_final: 0.7907 (t0) REVERT: A 956 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9038 (tm-30) REVERT: A 983 MET cc_start: 0.9340 (ttm) cc_final: 0.9031 (ttm) REVERT: A 1017 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9256 (tptm) REVERT: A 1018 MET cc_start: 0.9530 (mtm) cc_final: 0.9251 (mtm) REVERT: A 1289 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8973 (mm) REVERT: A 1306 ARG cc_start: 0.9427 (OUTLIER) cc_final: 0.9113 (mmt-90) outliers start: 33 outliers final: 24 residues processed: 73 average time/residue: 0.2578 time to fit residues: 27.4549 Evaluate side-chains 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 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 934 THR Chi-restraints excluded: chain A residue 1017 LYS 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 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3281 r_free = 0.3281 target = 0.051518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035015 restraints weight = 68754.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036093 restraints weight = 32448.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.036730 restraints weight = 21480.705| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11874 Z= 0.125 Angle : 0.562 13.630 16347 Z= 0.286 Chirality : 0.039 0.200 1816 Planarity : 0.003 0.042 1852 Dihedral : 18.325 149.846 2219 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 2.83 % Allowed : 20.89 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1219 helix: 2.23 (0.22), residues: 604 sheet: -0.62 (0.42), residues: 154 loop : 0.25 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.003 0.001 HIS A1269 PHE 0.011 0.001 PHE A 496 TYR 0.013 0.001 TYR A 61 ARG 0.008 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 561) hydrogen bonds : angle 3.76006 ( 1543) covalent geometry : bond 0.00281 (11874) covalent geometry : angle 0.56215 (16347) *********************** 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 73 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 51 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9005 (tppt) REVERT: A 307 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: A 353 PHE cc_start: 0.9223 (m-10) cc_final: 0.8990 (m-80) REVERT: A 507 MET cc_start: 0.9387 (ppp) cc_final: 0.8967 (ppp) REVERT: A 544 TRP cc_start: 0.9191 (OUTLIER) cc_final: 0.8456 (m100) REVERT: A 600 ASP cc_start: 0.9236 (t0) cc_final: 0.8861 (t0) REVERT: A 786 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 908 ASP cc_start: 0.8447 (t0) cc_final: 0.7903 (t0) REVERT: A 956 GLN cc_start: 0.9572 (mm-40) cc_final: 0.8989 (tm-30) REVERT: A 983 MET cc_start: 0.9207 (ttm) cc_final: 0.8988 (ttm) REVERT: A 1013 GLN cc_start: 0.9472 (mt0) cc_final: 0.9068 (mt0) REVERT: A 1017 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9238 (tptm) REVERT: A 1018 MET cc_start: 0.9517 (mtm) cc_final: 0.9215 (mtm) REVERT: A 1289 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (mm) REVERT: A 1306 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8992 (mmt-90) outliers start: 31 outliers final: 22 residues processed: 70 average time/residue: 0.2355 time to fit residues: 24.9471 Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 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 909 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1017 LYS 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 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3251 r_free = 0.3251 target = 0.051034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.034262 restraints weight = 69843.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035324 restraints weight = 33219.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.035941 restraints weight = 22246.419| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11874 Z= 0.171 Angle : 0.578 13.251 16347 Z= 0.298 Chirality : 0.040 0.148 1816 Planarity : 0.003 0.041 1852 Dihedral : 18.364 149.132 2219 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 2.74 % Allowed : 20.89 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1219 helix: 2.19 (0.22), residues: 610 sheet: -0.66 (0.42), residues: 154 loop : 0.27 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.004 0.001 HIS A1269 PHE 0.009 0.001 PHE A 245 TYR 0.016 0.001 TYR A 61 ARG 0.007 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 561) hydrogen bonds : angle 3.85514 ( 1543) covalent geometry : bond 0.00379 (11874) covalent geometry : angle 0.57760 (16347) ********************** 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 71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8037 (tpt) cc_final: 0.7746 (tpt) REVERT: A 20 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 307 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8381 (ptmm) REVERT: A 353 PHE cc_start: 0.9225 (m-10) cc_final: 0.9005 (m-80) REVERT: A 507 MET cc_start: 0.9363 (ppp) cc_final: 0.8984 (ppp) REVERT: A 544 TRP cc_start: 0.9326 (OUTLIER) cc_final: 0.8542 (m100) REVERT: A 600 ASP cc_start: 0.9254 (t0) cc_final: 0.8839 (t0) REVERT: A 604 MET cc_start: 0.9469 (mmm) cc_final: 0.8870 (mmm) REVERT: A 786 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 908 ASP cc_start: 0.8448 (t0) cc_final: 0.7876 (t0) REVERT: A 956 GLN cc_start: 0.9553 (mm-40) cc_final: 0.8958 (tm-30) REVERT: A 983 MET cc_start: 0.9314 (ttm) cc_final: 0.9056 (ttm) REVERT: A 1013 GLN cc_start: 0.9496 (mt0) cc_final: 0.9077 (mt0) REVERT: A 1017 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9224 (tptm) REVERT: A 1018 MET cc_start: 0.9543 (mtm) cc_final: 0.9246 (mtm) REVERT: A 1289 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 1306 ARG cc_start: 0.9408 (OUTLIER) cc_final: 0.9041 (mmt-90) outliers start: 30 outliers final: 24 residues processed: 68 average time/residue: 0.2512 time to fit residues: 26.0680 Evaluate side-chains 70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 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 909 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1017 LYS 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 1280 HIS Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1306 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3305 r_free = 0.3305 target = 0.052335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035846 restraints weight = 68352.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.036916 restraints weight = 32700.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037577 restraints weight = 21574.507| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 11874 Z= 0.106 Angle : 0.559 13.734 16347 Z= 0.283 Chirality : 0.039 0.155 1816 Planarity : 0.003 0.040 1852 Dihedral : 18.236 148.120 2219 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 21.62 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1219 helix: 2.23 (0.22), residues: 605 sheet: -0.52 (0.42), residues: 154 loop : 0.34 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.002 0.000 HIS A 754 PHE 0.014 0.001 PHE A 496 TYR 0.010 0.001 TYR A 173 ARG 0.007 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 561) hydrogen bonds : angle 3.71446 ( 1543) covalent geometry : bond 0.00242 (11874) covalent geometry : angle 0.55947 (16347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.20 seconds wall clock time: 86 minutes 57.76 seconds (5217.76 seconds total)