Starting phenix.real_space_refine on Thu Aug 6 01:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2026/8sfn_40445.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 103 5.49 5 S 26 5.16 5 C 7836 2.51 5 N 2195 2.21 5 O 2647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 10652 Classifications: {'peptide': 1302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1252} Chain breaks: 1 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 761 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 29} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 2.10, per 1000 atoms: 0.16 Number of scatterers: 12807 At special positions: 0 Unit cell: (102.484, 94.9848, 135.812, 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 26 16.00 P 103 15.00 O 2647 8.00 N 2195 7.00 C 7836 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: 1.03 Conformation dependent library (CDL) restraints added in 442.5 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 54.3% alpha, 13.0% beta 37 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.544A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.657A pdb=" N SER A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.934A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.031A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 197 through 215 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.875A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.594A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.935A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 removed outlier: 4.001A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 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: 3.906A pdb=" N ILE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 413 removed outlier: 4.036A pdb=" N VAL A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.523A pdb=" N ILE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.997A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 484 removed outlier: 3.811A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.322A pdb=" N LEU A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.671A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 639 through 647 removed outlier: 4.798A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 removed outlier: 3.770A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.505A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.878A 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 819 through 831 removed outlier: 3.741A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 4.221A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 4.391A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1010 through 1024 removed outlier: 3.628A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 removed outlier: 3.566A pdb=" N GLU A1181 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 3.979A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 removed outlier: 3.882A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1283 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.737A pdb=" N ILE A 265 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 811 removed outlier: 3.766A pdb=" N ASN A 808 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 850 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 930 removed outlier: 6.729A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 918 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1106 removed outlier: 6.701A pdb=" N HIS A1116 " --> pdb=" O ASP A1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A1104 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A1114 " --> pdb=" O LEU A1104 " (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 1161 through 1162 removed outlier: 3.590A pdb=" N VAL A1161 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1227 removed outlier: 4.290A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.40 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: 3357 1.34 - 1.46: 3240 1.46 - 1.58: 6456 1.58 - 1.70: 207 1.70 - 1.82: 44 Bond restraints: 13304 Sorted by residual: bond pdb=" C1' DC C 10 " pdb=" N1 DC C 10 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C3' DC C 10 " pdb=" C2' DC C 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA D 21 " pdb=" C2' DA D 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 bond pdb=" C3' DG D 29 " pdb=" C2' DG D 29 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 bond pdb=" C3' DC C 35 " pdb=" C2' DC C 35 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.84e+00 ... (remaining 13299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 18270 5.65 - 11.29: 142 11.29 - 16.94: 16 16.94 - 22.59: 5 22.59 - 28.23: 1 Bond angle restraints: 18434 Sorted by residual: angle pdb=" CA PRO A1178 " pdb=" N PRO A1178 " pdb=" CD PRO A1178 " ideal model delta sigma weight residual 112.00 96.92 15.08 1.40e+00 5.10e-01 1.16e+02 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 136.23 -28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O3' DA D 20 " pdb=" P DA D 21 " pdb=" OP1 DA D 21 " ideal model delta sigma weight residual 108.00 129.72 -21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 117.70 125.29 -7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" O3' DA D 21 " pdb=" P DG D 22 " pdb=" OP1 DG D 22 " ideal model delta sigma weight residual 108.00 126.71 -18.71 3.00e+00 1.11e-01 3.89e+01 ... (remaining 18429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 7289 35.13 - 70.27: 570 70.27 - 105.40: 33 105.40 - 140.53: 2 140.53 - 175.66: 5 Dihedral angle restraints: 7899 sinusoidal: 4053 harmonic: 3846 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 47.25 152.75 1 1.50e+01 4.44e-03 8.06e+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 67.59 132.41 1 1.50e+01 4.44e-03 7.14e+01 dihedral pdb=" CA TYR A 746 " pdb=" C TYR A 746 " pdb=" N ASN A 747 " pdb=" CA ASN A 747 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 7896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 2004 0.155 - 0.309: 22 0.309 - 0.463: 21 0.463 - 0.618: 3 0.618 - 0.772: 3 Chirality restraints: 2053 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.34 -3.11 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" P DA D 21 " pdb=" OP1 DA D 21 " pdb=" OP2 DA D 21 " pdb=" O5' DA D 21 " both_signs ideal model delta sigma weight residual True 2.34 -3.02 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" P DG D 22 " pdb=" OP1 DG D 22 " pdb=" OP2 DG D 22 " pdb=" O5' DG D 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.66e+00 ... (remaining 2050 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1177 " -0.134 5.00e-02 4.00e+02 1.89e-01 5.69e+01 pdb=" N PRO A1178 " 0.325 5.00e-02 4.00e+02 pdb=" CA PRO A1178 " -0.101 5.00e-02 4.00e+02 pdb=" CD PRO A1178 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1041 " 0.068 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A1042 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A1042 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1042 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 184 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP A 184 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP A 184 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 185 " -0.021 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 811 2.73 - 3.27: 12732 3.27 - 3.82: 23450 3.82 - 4.36: 27512 4.36 - 4.90: 42953 Nonbonded interactions: 107458 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.188 3.040 nonbonded pdb=" O CYS A 334 " pdb=" OG1 THR A 338 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 595 " pdb=" O LEU A 781 " model vdw 2.277 3.040 nonbonded pdb=" O TYR A 11 " pdb=" NE2 GLN A1044 " model vdw 2.292 3.120 nonbonded pdb=" O ILE A1073 " pdb=" ND2 ASN A1265 " model vdw 2.299 3.120 ... (remaining 107453 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 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 : 0.006 0.133 13304 Z= 0.353 Angle : 1.258 28.234 18434 Z= 0.701 Chirality : 0.076 0.772 2053 Planarity : 0.008 0.189 1998 Dihedral : 21.535 175.662 5409 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.26 % Allowed : 26.93 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1298 helix: -0.61 (0.19), residues: 613 sheet: -0.69 (0.42), residues: 148 loop : -1.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 386 TYR 0.039 0.002 TYR A 971 PHE 0.029 0.002 PHE A 999 TRP 0.057 0.003 TRP A 483 HIS 0.024 0.002 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.35 (13304) covalent geometry : angle 1.25833 / 0.70 (18434) hydrogen bonds : bond 0.15103 / 9.97 ( 606) hydrogen bonds : angle 7.07488 / 4.89 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 999 PHE cc_start: 0.6747 (t80) cc_final: 0.5837 (t80) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.0989 time to fit residues: 15.5782 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN A 9 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 913 ASN A 929 GLN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.071979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049860 restraints weight = 68614.484| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.10 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13304 Z= 0.227 Angle : 0.740 9.720 18434 Z= 0.399 Chirality : 0.045 0.336 2053 Planarity : 0.005 0.092 1998 Dihedral : 21.954 171.788 2718 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.40 % Allowed : 24.19 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1298 helix: 0.57 (0.20), residues: 623 sheet: -0.92 (0.44), residues: 138 loop : -0.64 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.022 0.002 TYR A 61 PHE 0.018 0.002 PHE A 198 TRP 0.012 0.001 TRP A 765 HIS 0.011 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (13304) covalent geometry : angle 0.73975 / 0.40 (18434) hydrogen bonds : bond 0.04742 / 3.14 ( 606) hydrogen bonds : angle 5.17209 / 3.51 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 1012 TYR cc_start: 0.7715 (m-80) cc_final: 0.7466 (m-80) outliers start: 28 outliers final: 13 residues processed: 112 average time/residue: 0.0811 time to fit residues: 14.2148 Evaluate side-chains 94 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** 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 = 0.3758 r_free = 0.3758 target = 0.073144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050975 restraints weight = 67820.476| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 5.12 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13304 Z= 0.134 Angle : 0.653 12.366 18434 Z= 0.351 Chirality : 0.043 0.358 2053 Planarity : 0.004 0.067 1998 Dihedral : 21.898 176.408 2716 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.32 % Allowed : 23.67 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.23), residues: 1298 helix: 0.96 (0.21), residues: 621 sheet: -0.90 (0.44), residues: 136 loop : -0.58 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.023 0.002 TYR A 61 PHE 0.014 0.001 PHE A 198 TRP 0.011 0.001 TRP A1298 HIS 0.010 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (13304) covalent geometry : angle 0.65319 / 0.35 (18434) hydrogen bonds : bond 0.04162 / 2.75 ( 606) hydrogen bonds : angle 4.75381 / 3.22 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8761 (t80) cc_final: 0.8538 (t80) REVERT: A 732 MET cc_start: 0.9149 (tmm) cc_final: 0.8826 (tmm) REVERT: A 1012 TYR cc_start: 0.7713 (m-80) cc_final: 0.7466 (m-80) outliers start: 27 outliers final: 15 residues processed: 109 average time/residue: 0.0882 time to fit residues: 14.8781 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1148 ASP Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.069721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047443 restraints weight = 70099.016| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 5.11 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13304 Z= 0.253 Angle : 0.700 12.032 18434 Z= 0.380 Chirality : 0.045 0.279 2053 Planarity : 0.004 0.053 1998 Dihedral : 22.035 179.960 2716 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.92 % Allowed : 23.24 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1298 helix: 1.17 (0.21), residues: 627 sheet: -1.10 (0.42), residues: 141 loop : -0.41 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1242 TYR 0.020 0.002 TYR A 829 PHE 0.018 0.002 PHE A1079 TRP 0.009 0.001 TRP A1258 HIS 0.009 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (13304) covalent geometry : angle 0.70048 / 0.38 (18434) hydrogen bonds : bond 0.04560 / 3.02 ( 606) hydrogen bonds : angle 4.77754 / 3.26 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 MET cc_start: 0.9158 (tmm) cc_final: 0.8800 (tmm) REVERT: A 999 PHE cc_start: 0.9232 (t80) cc_final: 0.8177 (t80) REVERT: A 1014 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 1083 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8631 (m-10) outliers start: 34 outliers final: 23 residues processed: 99 average time/residue: 0.0905 time to fit residues: 13.7580 Evaluate side-chains 93 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 11 optimal weight: 0.0010 chunk 117 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 36 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3723 r_free = 0.3723 target = 0.071078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048755 restraints weight = 69108.688| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.15 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13304 Z= 0.140 Angle : 0.643 13.352 18434 Z= 0.345 Chirality : 0.042 0.294 2053 Planarity : 0.004 0.047 1998 Dihedral : 21.975 177.412 2716 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 23.67 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1298 helix: 1.30 (0.21), residues: 627 sheet: -1.03 (0.43), residues: 137 loop : -0.34 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 725 TYR 0.022 0.002 TYR A1012 PHE 0.016 0.001 PHE A 198 TRP 0.008 0.001 TRP A 765 HIS 0.007 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (13304) covalent geometry : angle 0.64345 / 0.34 (18434) hydrogen bonds : bond 0.03971 / 2.63 ( 606) hydrogen bonds : angle 4.55241 / 3.11 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 732 MET cc_start: 0.9201 (tmm) cc_final: 0.8823 (tmm) REVERT: A 1014 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8401 (pp30) outliers start: 29 outliers final: 17 residues processed: 99 average time/residue: 0.0910 time to fit residues: 14.0075 Evaluate side-chains 91 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 23 optimal weight: 6.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3713 r_free = 0.3713 target = 0.070795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048784 restraints weight = 68812.564| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 5.08 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13304 Z= 0.160 Angle : 0.639 13.061 18434 Z= 0.342 Chirality : 0.042 0.274 2053 Planarity : 0.004 0.042 1998 Dihedral : 21.926 175.001 2716 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 24.70 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1298 helix: 1.37 (0.21), residues: 627 sheet: -1.00 (0.42), residues: 141 loop : -0.31 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1174 TYR 0.023 0.002 TYR A 61 PHE 0.015 0.001 PHE A 198 TRP 0.016 0.001 TRP A1298 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (13304) covalent geometry : angle 0.63865 / 0.34 (18434) hydrogen bonds : bond 0.03917 / 2.60 ( 606) hydrogen bonds : angle 4.54073 / 3.11 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8253 (mm) REVERT: A 732 MET cc_start: 0.9186 (tmm) cc_final: 0.8809 (tmm) REVERT: A 999 PHE cc_start: 0.9204 (t80) cc_final: 0.8478 (t80) REVERT: A 1012 TYR cc_start: 0.7814 (m-80) cc_final: 0.7530 (m-80) outliers start: 26 outliers final: 21 residues processed: 93 average time/residue: 0.0905 time to fit residues: 13.1268 Evaluate side-chains 93 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3719 r_free = 0.3719 target = 0.071050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048993 restraints weight = 68880.072| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 5.07 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13304 Z= 0.143 Angle : 0.644 13.738 18434 Z= 0.342 Chirality : 0.043 0.534 2053 Planarity : 0.004 0.045 1998 Dihedral : 21.878 173.229 2716 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.57 % Allowed : 24.19 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1298 helix: 1.42 (0.21), residues: 627 sheet: -0.97 (0.42), residues: 141 loop : -0.29 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1003 TYR 0.026 0.002 TYR A 61 PHE 0.014 0.001 PHE A 198 TRP 0.011 0.001 TRP A 765 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13304) covalent geometry : angle 0.64416 / 0.34 (18434) hydrogen bonds : bond 0.03821 / 2.54 ( 606) hydrogen bonds : angle 4.48520 / 3.08 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8257 (mm) REVERT: A 624 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9009 (t) REVERT: A 732 MET cc_start: 0.9194 (tmm) cc_final: 0.8809 (tmm) outliers start: 30 outliers final: 21 residues processed: 97 average time/residue: 0.0885 time to fit residues: 13.2725 Evaluate side-chains 95 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 11 optimal weight: 0.0010 chunk 66 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3714 r_free = 0.3714 target = 0.071100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.049070 restraints weight = 69200.957| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 5.12 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13304 Z= 0.149 Angle : 0.640 13.313 18434 Z= 0.341 Chirality : 0.042 0.384 2053 Planarity : 0.004 0.042 1998 Dihedral : 21.771 172.379 2716 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.66 % Allowed : 24.36 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1298 helix: 1.46 (0.21), residues: 626 sheet: -1.02 (0.42), residues: 141 loop : -0.29 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1174 TYR 0.025 0.002 TYR A 61 PHE 0.015 0.001 PHE A 198 TRP 0.014 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (13304) covalent geometry : angle 0.63990 / 0.34 (18434) hydrogen bonds : bond 0.03770 / 2.49 ( 606) hydrogen bonds : angle 4.45255 / 3.06 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 624 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9007 (t) REVERT: A 732 MET cc_start: 0.9199 (tmm) cc_final: 0.8802 (tmm) REVERT: A 1083 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8660 (m-10) outliers start: 31 outliers final: 22 residues processed: 96 average time/residue: 0.0822 time to fit residues: 12.3734 Evaluate side-chains 97 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 137 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.070813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048878 restraints weight = 69364.822| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.07 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13304 Z= 0.157 Angle : 0.643 13.018 18434 Z= 0.343 Chirality : 0.043 0.315 2053 Planarity : 0.004 0.052 1998 Dihedral : 21.725 172.680 2716 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.57 % Allowed : 24.70 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1298 helix: 1.48 (0.21), residues: 622 sheet: -0.83 (0.45), residues: 131 loop : -0.33 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.022 0.001 TYR A 61 PHE 0.015 0.001 PHE A 198 TRP 0.013 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (13304) covalent geometry : angle 0.64251 / 0.34 (18434) hydrogen bonds : bond 0.03807 / 2.52 ( 606) hydrogen bonds : angle 4.45931 / 3.07 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 624 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9011 (t) REVERT: A 732 MET cc_start: 0.9195 (tmm) cc_final: 0.8803 (tmm) REVERT: A 778 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9199 (t) outliers start: 30 outliers final: 22 residues processed: 94 average time/residue: 0.0807 time to fit residues: 11.9594 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 122 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3700 r_free = 0.3700 target = 0.070227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048242 restraints weight = 69779.245| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 5.06 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13304 Z= 0.174 Angle : 0.652 12.849 18434 Z= 0.349 Chirality : 0.043 0.290 2053 Planarity : 0.004 0.050 1998 Dihedral : 21.721 172.801 2716 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 24.61 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1298 helix: 1.51 (0.21), residues: 621 sheet: -0.86 (0.45), residues: 131 loop : -0.33 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.024 0.002 TYR A 61 PHE 0.017 0.001 PHE A 198 TRP 0.012 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (13304) covalent geometry : angle 0.65168 / 0.35 (18434) hydrogen bonds : bond 0.03842 / 2.54 ( 606) hydrogen bonds : angle 4.46997 / 3.08 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 624 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9013 (t) REVERT: A 732 MET cc_start: 0.9198 (tmm) cc_final: 0.8816 (tmm) REVERT: A 778 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9218 (t) REVERT: A 1083 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8795 (m-10) REVERT: A 1176 LEU cc_start: 0.9098 (tt) cc_final: 0.8855 (mp) outliers start: 29 outliers final: 22 residues processed: 93 average time/residue: 0.0824 time to fit residues: 11.8292 Evaluate side-chains 98 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** 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 = 0.3706 r_free = 0.3706 target = 0.070453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048273 restraints weight = 69561.338| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 5.06 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13304 Z= 0.160 Angle : 0.652 13.173 18434 Z= 0.349 Chirality : 0.042 0.273 2053 Planarity : 0.004 0.077 1998 Dihedral : 21.701 173.153 2716 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 25.21 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1298 helix: 1.53 (0.21), residues: 621 sheet: -0.64 (0.46), residues: 125 loop : -0.29 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1174 TYR 0.022 0.001 TYR A 61 PHE 0.015 0.001 PHE A 198 TRP 0.013 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (13304) covalent geometry : angle 0.65190 / 0.35 (18434) hydrogen bonds : bond 0.03773 / 2.49 ( 606) hydrogen bonds : angle 4.42318 / 3.05 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.67 seconds wall clock time: 44 minutes 33.96 seconds (2673.96 seconds total)