Starting phenix.real_space_refine on Fri Aug 7 03:28:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cji_45632/08_2026/9cji_45632.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9427 atoms to isotropic. 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 67 5.49 5 S 27 5.16 5 C 7120 2.51 5 N 1961 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 11477 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 528 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 19} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 436 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 10085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1244, 10085 Classifications: {'peptide': 1244} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 47, 'TRANS': 1196} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 2.00, per 1000 atoms: 0.17 Number of scatterers: 11477 At special positions: 0 Unit cell: (98.12, 108.155, 138.26, 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 27 16.00 P 67 15.00 O 2302 8.00 N 1961 7.00 C 7120 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 421.3 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 54.8% alpha, 11.7% beta 26 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.518A 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 68 removed outlier: 4.134A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 4.180A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.823A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.751A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 133 No H-bonds generated for 'chain 'A' and resid 132 through 133' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 146 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: 3.523A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.528A pdb=" N ASP A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.787A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.234A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 325 through 344 removed outlier: 4.067A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.548A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.729A pdb=" N HIS A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 367 through 379 removed outlier: 4.678A pdb=" N GLU A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 removed outlier: 4.626A pdb=" N ARG A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.566A pdb=" N LYS A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 451 removed outlier: 4.167A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.657A pdb=" N ILE A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 482 " --> pdb=" O TYR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.308A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.806A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 4.239A 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 694 through 698 removed outlier: 3.690A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 698 " --> pdb=" O LEU A 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 694 through 698' Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.546A pdb=" N TYR A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Proline residue: A 716 - end of helix removed outlier: 3.782A pdb=" N TYR A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.734A 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: 3.555A pdb=" N ASN A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 943 through 956 Processing helix chain 'A' and resid 958 through 987 Processing helix chain 'A' and resid 1010 through 1025 removed outlier: 4.043A pdb=" N GLN A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 4.182A pdb=" N PHE A1101 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1189 removed outlier: 3.661A pdb=" N GLU A1181 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1207 Processing helix chain 'A' and resid 1208 through 1224 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 1284 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.098A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 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 589 through 596 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 799 through 800 removed outlier: 3.535A pdb=" N ILE A 858 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 811 removed outlier: 5.761A pdb=" N ILE A 850 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.612A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1103 through 1107 removed outlier: 4.144A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A1112 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AB2, first strand: chain 'A' and resid 1159 through 1161 Processing sheet with id=AB3, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.687A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1909 1.32 - 1.45: 3475 1.45 - 1.57: 6313 1.57 - 1.70: 130 1.70 - 1.82: 44 Bond restraints: 11871 Sorted by residual: bond pdb=" O5' 2YR C 7 " pdb=" P 2YR C 7 " ideal model delta sigma weight residual 1.721 1.598 0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C1' DT C 2 " pdb=" N1 DT C 2 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG D 16 " pdb=" C2' DG D 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" N THR A 522 " pdb=" CA THR A 522 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.22e-02 6.72e+03 9.36e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 15872 1.69 - 3.38: 398 3.38 - 5.07: 53 5.07 - 6.76: 11 6.76 - 8.45: 8 Bond angle restraints: 16342 Sorted by residual: angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 102.20 3.80 6.00e-01 2.78e+00 4.01e+01 angle pdb=" N TYR A 47 " pdb=" CA TYR A 47 " pdb=" C TYR A 47 " ideal model delta sigma weight residual 111.03 104.40 6.63 1.11e+00 8.12e-01 3.57e+01 angle pdb=" C LYS A 48 " pdb=" N GLU A 49 " pdb=" CA GLU A 49 " ideal model delta sigma weight residual 120.29 111.84 8.45 1.42e+00 4.96e-01 3.54e+01 angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 113.20 106.21 6.99 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N ILE A1164 " pdb=" CA ILE A1164 " pdb=" C ILE A1164 " ideal model delta sigma weight residual 111.62 108.04 3.58 7.90e-01 1.60e+00 2.05e+01 ... (remaining 16337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6694 35.92 - 71.84: 349 71.84 - 107.75: 21 107.75 - 143.67: 1 143.67 - 179.59: 2 Dihedral angle restraints: 7067 sinusoidal: 3392 harmonic: 3675 Sorted by residual: dihedral pdb=" O4' U B 16 " pdb=" C1' U B 16 " pdb=" N1 U B 16 " pdb=" C2 U B 16 " ideal model delta sinusoidal sigma weight residual 232.00 57.84 174.16 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA PHE A 598 " pdb=" C PHE A 598 " pdb=" N PRO A 599 " pdb=" CA PRO A 599 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C4' DT C 5 " pdb=" C3' DT C 5 " pdb=" O3' DT C 5 " pdb=" P DG C 6 " ideal model delta sinusoidal sigma weight residual -140.00 39.59 -179.59 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1479 0.052 - 0.103: 275 0.103 - 0.155: 60 0.155 - 0.206: 3 0.206 - 0.258: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C3' 2YR C 7 " pdb=" C2' 2YR C 7 " pdb=" C4' 2YR C 7 " pdb=" O3' 2YR C 7 " both_signs ideal model delta sigma weight residual False -2.57 -2.78 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA HIS A 46 " pdb=" N HIS A 46 " pdb=" C HIS A 46 " pdb=" CB HIS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1816 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2YR C 7 " -0.139 2.00e-02 2.50e+03 2.12e-01 1.12e+03 pdb=" C2 2YR C 7 " -0.023 2.00e-02 2.50e+03 pdb=" C4 2YR C 7 " 0.187 2.00e-02 2.50e+03 pdb=" C5 2YR C 7 " 0.182 2.00e-02 2.50e+03 pdb=" C6 2YR C 7 " 0.074 2.00e-02 2.50e+03 pdb=" C9 2YR C 7 " -0.506 2.00e-02 2.50e+03 pdb=" N1 2YR C 7 " -0.028 2.00e-02 2.50e+03 pdb=" N3 2YR C 7 " 0.084 2.00e-02 2.50e+03 pdb=" N4 2YR C 7 " 0.281 2.00e-02 2.50e+03 pdb=" O2 2YR C 7 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 43 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ARG A 43 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG A 43 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 44 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 518 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ARG A 518 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG A 518 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 519 " 0.018 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 0.52 - 1.40: 2 1.40 - 2.27: 11 2.27 - 3.15: 9118 3.15 - 4.02: 30716 4.02 - 4.90: 55342 Warning: very small nonbonded interaction distances. Nonbonded interactions: 95189 Sorted by model distance: nonbonded pdb=" CE2 PHE A 165 " pdb=" OD1 ASN A 534 " model vdw 0.519 3.340 nonbonded pdb=" CE2 PHE A 165 " pdb=" CG ASN A 534 " model vdw 1.162 3.570 nonbonded pdb=" CB LYS A 164 " pdb=" CG PRO A 538 " model vdw 1.493 3.840 nonbonded pdb=" CD2 PHE A 165 " pdb=" OD1 ASN A 534 " model vdw 1.593 3.340 nonbonded pdb=" CB LYS A 164 " pdb=" CB PRO A 538 " model vdw 1.608 3.840 ... (remaining 95184 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 0.004 0.182 11874 Z= 0.304 Angle : 0.616 8.453 16342 Z= 0.431 Chirality : 0.044 0.258 1819 Planarity : 0.006 0.212 1861 Dihedral : 18.761 179.588 4689 Min Nonbonded Distance : 0.519 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.83 % Allowed : 2.02 % Favored : 97.15 % 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: -0.08 (0.24), residues: 1238 helix: 0.15 (0.21), residues: 591 sheet: -0.63 (0.44), residues: 153 loop : 0.16 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1168 TYR 0.020 0.001 TYR A 520 PHE 0.011 0.001 PHE A 598 TRP 0.008 0.001 TRP A 382 HIS 0.011 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.25 (11871) covalent geometry : angle 0.61627 / 0.43 (16342) hydrogen bonds : bond 0.18460 / 20.40 ( 571) hydrogen bonds : angle 6.99843 / 9.05 ( 1574) Misc. bond : bond 0.10943 / 10.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7620 (m) cc_final: 0.7000 (p) REVERT: A 9 ASN cc_start: 0.7686 (t0) cc_final: 0.7323 (t0) REVERT: A 523 LYS cc_start: 0.6992 (pttp) cc_final: 0.6613 (pttp) REVERT: A 528 VAL cc_start: 0.7809 (t) cc_final: 0.7515 (t) REVERT: A 568 MET cc_start: 0.7740 (mpp) cc_final: 0.7254 (mtm) REVERT: A 594 TYR cc_start: 0.8179 (m-80) cc_final: 0.7930 (m-80) REVERT: A 631 ASN cc_start: 0.6958 (m-40) cc_final: 0.6670 (m-40) REVERT: A 655 PHE cc_start: 0.7452 (m-10) cc_final: 0.6965 (m-10) REVERT: A 673 LEU cc_start: 0.7908 (tt) cc_final: 0.7604 (mm) REVERT: A 674 CYS cc_start: 0.7245 (m) cc_final: 0.6905 (t) REVERT: A 678 ASP cc_start: 0.6736 (m-30) cc_final: 0.6415 (m-30) REVERT: A 757 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7418 (mtmm) REVERT: A 772 GLU cc_start: 0.7054 (pm20) cc_final: 0.6826 (pm20) REVERT: A 784 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7303 (mm-40) REVERT: A 809 LYS cc_start: 0.7381 (mttt) cc_final: 0.7172 (mttp) REVERT: A 843 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.7038 (tpp80) REVERT: A 848 ASN cc_start: 0.7547 (t0) cc_final: 0.7286 (t0) REVERT: A 854 VAL cc_start: 0.8244 (t) cc_final: 0.8000 (p) REVERT: A 860 LYS cc_start: 0.8052 (tttp) cc_final: 0.7671 (tttm) REVERT: A 1006 ILE cc_start: 0.7583 (mm) cc_final: 0.7288 (mm) REVERT: A 1021 ASP cc_start: 0.7402 (m-30) cc_final: 0.7121 (m-30) REVERT: A 1031 TYR cc_start: 0.8322 (m-10) cc_final: 0.7969 (m-80) REVERT: A 1071 SER cc_start: 0.8434 (t) cc_final: 0.8032 (p) REVERT: A 1072 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7326 (mmtm) REVERT: A 1096 HIS cc_start: 0.6336 (m90) cc_final: 0.6040 (m90) REVERT: A 1141 GLU cc_start: 0.6517 (mm-30) cc_final: 0.5057 (mm-30) REVERT: A 1142 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7586 (ttpp) REVERT: A 1239 SER cc_start: 0.7340 (t) cc_final: 0.6814 (p) REVERT: A 1242 ARG cc_start: 0.6922 (mtt-85) cc_final: 0.6658 (mtt-85) REVERT: A 1279 ASN cc_start: 0.7944 (m-40) cc_final: 0.7742 (m-40) outliers start: 9 outliers final: 2 residues processed: 206 average time/residue: 0.1246 time to fit residues: 34.6753 Evaluate side-chains 172 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 346 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 552 ASN A 831 ASN A1116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148824 restraints weight = 17007.493| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.31 r_work: 0.3435 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11874 Z= 0.178 Angle : 0.605 8.376 16342 Z= 0.324 Chirality : 0.044 0.267 1819 Planarity : 0.004 0.036 1861 Dihedral : 20.141 179.503 2204 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.74 % Allowed : 8.91 % Favored : 89.35 % 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: 0.84 (0.25), residues: 1238 helix: 1.32 (0.21), residues: 597 sheet: -0.47 (0.42), residues: 165 loop : 0.13 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1226 TYR 0.019 0.002 TYR A 520 PHE 0.049 0.002 PHE A 165 TRP 0.013 0.001 TRP A 958 HIS 0.010 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (11871) covalent geometry : angle 0.60498 / 0.32 (16342) hydrogen bonds : bond 0.05015 / 5.59 ( 571) hydrogen bonds : angle 4.95148 / 6.30 ( 1574) Misc. bond : bond 0.00851 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8357 (t0) cc_final: 0.7775 (t0) REVERT: A 34 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8249 (mm-40) REVERT: A 523 LYS cc_start: 0.7400 (pttp) cc_final: 0.7062 (pttp) REVERT: A 536 GLN cc_start: 0.8191 (mp10) cc_final: 0.7922 (mp10) REVERT: A 550 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8196 (tmtt) REVERT: A 594 TYR cc_start: 0.8556 (m-80) cc_final: 0.8261 (m-80) REVERT: A 631 ASN cc_start: 0.7491 (m-40) cc_final: 0.7236 (m-40) REVERT: A 655 PHE cc_start: 0.7734 (m-10) cc_final: 0.7119 (m-10) REVERT: A 674 CYS cc_start: 0.8216 (m) cc_final: 0.7441 (t) REVERT: A 678 ASP cc_start: 0.7482 (m-30) cc_final: 0.7099 (m-30) REVERT: A 736 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7847 (tp30) REVERT: A 757 LYS cc_start: 0.8093 (ptpp) cc_final: 0.7842 (mtmm) REVERT: A 772 GLU cc_start: 0.7654 (pm20) cc_final: 0.7430 (pm20) REVERT: A 806 MET cc_start: 0.7620 (mtp) cc_final: 0.7295 (mtm) REVERT: A 843 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7588 (tpp80) REVERT: A 848 ASN cc_start: 0.7807 (t0) cc_final: 0.7421 (t0) REVERT: A 854 VAL cc_start: 0.8543 (t) cc_final: 0.8139 (p) REVERT: A 897 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8218 (mtpp) REVERT: A 901 GLU cc_start: 0.8514 (pt0) cc_final: 0.8234 (pm20) REVERT: A 1000 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7895 (mmmm) REVERT: A 1006 ILE cc_start: 0.7508 (mm) cc_final: 0.7257 (mm) REVERT: A 1021 ASP cc_start: 0.7817 (m-30) cc_final: 0.7581 (m-30) REVERT: A 1031 TYR cc_start: 0.8577 (m-10) cc_final: 0.8175 (m-80) REVERT: A 1069 TYR cc_start: 0.8252 (m-80) cc_final: 0.8050 (m-80) REVERT: A 1071 SER cc_start: 0.8643 (t) cc_final: 0.8341 (p) REVERT: A 1072 LYS cc_start: 0.7975 (mmtm) cc_final: 0.7703 (mmtm) REVERT: A 1096 HIS cc_start: 0.7633 (m90) cc_final: 0.7224 (m90) REVERT: A 1142 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8064 (ttpp) REVERT: A 1232 THR cc_start: 0.8315 (t) cc_final: 0.8086 (p) REVERT: A 1234 GLU cc_start: 0.7275 (tt0) cc_final: 0.7062 (tt0) REVERT: A 1242 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7542 (mtt-85) outliers start: 19 outliers final: 7 residues processed: 187 average time/residue: 0.1365 time to fit residues: 34.3282 Evaluate side-chains 174 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1099 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.190866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147944 restraints weight = 16940.755| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.29 r_work: 0.3460 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11874 Z= 0.184 Angle : 0.574 7.567 16342 Z= 0.308 Chirality : 0.043 0.286 1819 Planarity : 0.004 0.035 1861 Dihedral : 20.187 179.995 2202 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.93 % Allowed : 12.21 % Favored : 85.86 % 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: 1.07 (0.25), residues: 1238 helix: 1.66 (0.22), residues: 600 sheet: -0.49 (0.42), residues: 153 loop : 0.02 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 862 TYR 0.014 0.002 TYR A 789 PHE 0.025 0.002 PHE A 165 TRP 0.009 0.001 TRP A 958 HIS 0.011 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (11871) covalent geometry : angle 0.57449 / 0.31 (16342) hydrogen bonds : bond 0.04472 / 4.86 ( 571) hydrogen bonds : angle 4.55723 / 5.84 ( 1574) Misc. bond : bond 0.00138 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8277 (t0) cc_final: 0.7651 (t0) REVERT: A 32 GLN cc_start: 0.8384 (mt0) cc_final: 0.8141 (mt0) REVERT: A 34 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8227 (mm-40) REVERT: A 470 GLN cc_start: 0.7185 (mt0) cc_final: 0.6922 (mp10) REVERT: A 536 GLN cc_start: 0.8204 (mp10) cc_final: 0.7896 (mp10) REVERT: A 550 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8195 (tmtt) REVERT: A 585 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (ttpp) REVERT: A 604 MET cc_start: 0.8507 (mmm) cc_final: 0.7714 (mmm) REVERT: A 631 ASN cc_start: 0.7436 (m-40) cc_final: 0.7108 (m-40) REVERT: A 655 PHE cc_start: 0.7745 (m-10) cc_final: 0.7172 (m-10) REVERT: A 674 CYS cc_start: 0.8225 (m) cc_final: 0.7470 (t) REVERT: A 678 ASP cc_start: 0.7492 (m-30) cc_final: 0.7110 (m-30) REVERT: A 757 LYS cc_start: 0.8199 (ptpp) cc_final: 0.7963 (mtmm) REVERT: A 806 MET cc_start: 0.7820 (mtp) cc_final: 0.7579 (mtm) REVERT: A 843 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7530 (tpp80) REVERT: A 848 ASN cc_start: 0.7870 (t0) cc_final: 0.7489 (t0) REVERT: A 854 VAL cc_start: 0.8592 (t) cc_final: 0.8192 (p) REVERT: A 901 GLU cc_start: 0.8506 (pt0) cc_final: 0.8261 (pm20) REVERT: A 1000 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7796 (mmmm) REVERT: A 1021 ASP cc_start: 0.7821 (m-30) cc_final: 0.7589 (m-30) REVERT: A 1031 TYR cc_start: 0.8597 (m-10) cc_final: 0.8286 (m-80) REVERT: A 1071 SER cc_start: 0.8603 (t) cc_final: 0.8383 (p) REVERT: A 1072 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7894 (mmtm) REVERT: A 1096 HIS cc_start: 0.7521 (m90) cc_final: 0.7093 (m90) REVERT: A 1142 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8238 (ttpp) REVERT: A 1234 GLU cc_start: 0.7367 (tt0) cc_final: 0.7165 (tt0) REVERT: A 1242 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7384 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7305 (t70) cc_final: 0.7018 (t0) outliers start: 21 outliers final: 10 residues processed: 193 average time/residue: 0.1083 time to fit residues: 28.2136 Evaluate side-chains 183 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A1105 HIS A1116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148755 restraints weight = 16846.037| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.40 r_work: 0.3441 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11874 Z= 0.169 Angle : 0.546 7.104 16342 Z= 0.295 Chirality : 0.043 0.282 1819 Planarity : 0.004 0.036 1861 Dihedral : 20.140 178.557 2199 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.11 % Allowed : 14.05 % Favored : 83.84 % 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: 1.21 (0.25), residues: 1238 helix: 1.86 (0.22), residues: 599 sheet: -0.76 (0.42), residues: 152 loop : 0.11 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 955 TYR 0.016 0.002 TYR A1268 PHE 0.018 0.001 PHE A 165 TRP 0.010 0.001 TRP A 958 HIS 0.014 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (11871) covalent geometry : angle 0.54632 / 0.30 (16342) hydrogen bonds : bond 0.04106 / 4.44 ( 571) hydrogen bonds : angle 4.41394 / 5.64 ( 1574) Misc. bond : bond 0.00233 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8072 (t0) cc_final: 0.7438 (t0) REVERT: A 34 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8093 (mm-40) REVERT: A 470 GLN cc_start: 0.7085 (mt0) cc_final: 0.6776 (mp10) REVERT: A 523 LYS cc_start: 0.7279 (pttp) cc_final: 0.6926 (pttp) REVERT: A 536 GLN cc_start: 0.8073 (mp10) cc_final: 0.7753 (mp10) REVERT: A 558 VAL cc_start: 0.8361 (p) cc_final: 0.8035 (t) REVERT: A 585 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8091 (ttpp) REVERT: A 604 MET cc_start: 0.8391 (mmm) cc_final: 0.8087 (mmt) REVERT: A 655 PHE cc_start: 0.7625 (m-10) cc_final: 0.7042 (m-10) REVERT: A 662 LYS cc_start: 0.7447 (ptmt) cc_final: 0.7052 (ptmt) REVERT: A 674 CYS cc_start: 0.8012 (m) cc_final: 0.7278 (t) REVERT: A 678 ASP cc_start: 0.7263 (m-30) cc_final: 0.6897 (m-30) REVERT: A 843 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7402 (tpp80) REVERT: A 854 VAL cc_start: 0.8629 (t) cc_final: 0.8308 (p) REVERT: A 901 GLU cc_start: 0.8316 (pt0) cc_final: 0.8083 (pm20) REVERT: A 955 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7131 (mtp180) REVERT: A 1000 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7649 (mmmm) REVERT: A 1006 ILE cc_start: 0.7344 (mm) cc_final: 0.6917 (mt) REVERT: A 1021 ASP cc_start: 0.7643 (m-30) cc_final: 0.7409 (m-30) REVERT: A 1031 TYR cc_start: 0.8519 (m-10) cc_final: 0.8254 (m-80) REVERT: A 1071 SER cc_start: 0.8542 (t) cc_final: 0.8261 (p) REVERT: A 1072 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7766 (mmtm) REVERT: A 1096 HIS cc_start: 0.7215 (m90) cc_final: 0.6833 (m90) REVERT: A 1155 ILE cc_start: 0.8266 (mm) cc_final: 0.7891 (mm) REVERT: A 1250 ASP cc_start: 0.7074 (t70) cc_final: 0.6830 (t0) outliers start: 23 outliers final: 12 residues processed: 188 average time/residue: 0.1057 time to fit residues: 26.7451 Evaluate side-chains 186 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A 878 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147520 restraints weight = 16821.793| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.31 r_work: 0.3460 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11874 Z= 0.180 Angle : 0.555 7.565 16342 Z= 0.300 Chirality : 0.043 0.302 1819 Planarity : 0.004 0.034 1861 Dihedral : 20.099 176.880 2199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.11 % Allowed : 13.96 % Favored : 83.93 % 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: 1.33 (0.25), residues: 1238 helix: 1.96 (0.21), residues: 608 sheet: -0.59 (0.41), residues: 163 loop : 0.10 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 862 TYR 0.016 0.002 TYR A 595 PHE 0.015 0.001 PHE A 165 TRP 0.010 0.001 TRP A 958 HIS 0.015 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (11871) covalent geometry : angle 0.55452 / 0.30 (16342) hydrogen bonds : bond 0.04070 / 4.36 ( 571) hydrogen bonds : angle 4.29250 / 5.53 ( 1574) Misc. bond : bond 0.00165 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8242 (t0) cc_final: 0.7573 (t0) REVERT: A 34 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8205 (mm-40) REVERT: A 235 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.2461 (t) REVERT: A 470 GLN cc_start: 0.7318 (mt0) cc_final: 0.6988 (mp10) REVERT: A 536 GLN cc_start: 0.8201 (mp10) cc_final: 0.7946 (mp10) REVERT: A 585 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: A 604 MET cc_start: 0.8513 (mmm) cc_final: 0.8228 (mmt) REVERT: A 655 PHE cc_start: 0.7709 (m-10) cc_final: 0.7115 (m-10) REVERT: A 662 LYS cc_start: 0.7516 (ptmt) cc_final: 0.7118 (ptmt) REVERT: A 674 CYS cc_start: 0.8186 (m) cc_final: 0.7481 (t) REVERT: A 678 ASP cc_start: 0.7468 (m-30) cc_final: 0.7111 (m-30) REVERT: A 710 TYR cc_start: 0.8165 (t80) cc_final: 0.7812 (t80) REVERT: A 728 GLU cc_start: 0.7823 (tt0) cc_final: 0.7570 (tm-30) REVERT: A 843 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7585 (tpp80) REVERT: A 860 LYS cc_start: 0.8210 (tttm) cc_final: 0.7965 (tttm) REVERT: A 901 GLU cc_start: 0.8447 (pt0) cc_final: 0.8215 (pm20) REVERT: A 993 GLU cc_start: 0.7533 (pm20) cc_final: 0.7199 (pt0) REVERT: A 1000 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7733 (mmmm) REVERT: A 1021 ASP cc_start: 0.7843 (m-30) cc_final: 0.7615 (m-30) REVERT: A 1031 TYR cc_start: 0.8586 (m-10) cc_final: 0.8341 (m-80) REVERT: A 1071 SER cc_start: 0.8611 (t) cc_final: 0.8406 (p) REVERT: A 1072 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7959 (mmtm) REVERT: A 1096 HIS cc_start: 0.7521 (m90) cc_final: 0.7073 (m90) REVERT: A 1234 GLU cc_start: 0.7363 (tt0) cc_final: 0.7162 (tt0) REVERT: A 1278 LEU cc_start: 0.8157 (mt) cc_final: 0.7606 (mt) outliers start: 23 outliers final: 14 residues processed: 195 average time/residue: 0.1168 time to fit residues: 30.9379 Evaluate side-chains 193 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.189917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146621 restraints weight = 16837.822| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.35 r_work: 0.3386 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11874 Z= 0.176 Angle : 0.556 7.467 16342 Z= 0.298 Chirality : 0.043 0.305 1819 Planarity : 0.004 0.033 1861 Dihedral : 19.988 176.198 2199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.30 % Allowed : 15.06 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1238 helix: 1.96 (0.21), residues: 612 sheet: -0.64 (0.42), residues: 153 loop : 0.15 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 862 TYR 0.019 0.002 TYR A 109 PHE 0.031 0.002 PHE A1154 TRP 0.008 0.001 TRP A 958 HIS 0.006 0.001 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (11871) covalent geometry : angle 0.55558 / 0.30 (16342) hydrogen bonds : bond 0.03990 / 4.26 ( 571) hydrogen bonds : angle 4.26316 / 5.48 ( 1574) Misc. bond : bond 0.00098 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8256 (t0) cc_final: 0.7591 (t0) REVERT: A 34 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8238 (mm-40) REVERT: A 235 THR cc_start: 0.2703 (OUTLIER) cc_final: 0.2464 (t) REVERT: A 470 GLN cc_start: 0.7435 (mt0) cc_final: 0.7115 (mp10) REVERT: A 536 GLN cc_start: 0.8214 (mp10) cc_final: 0.7936 (mp10) REVERT: A 585 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: A 604 MET cc_start: 0.8496 (mmm) cc_final: 0.8208 (mmt) REVERT: A 655 PHE cc_start: 0.7710 (m-10) cc_final: 0.7133 (m-10) REVERT: A 662 LYS cc_start: 0.7526 (ptmt) cc_final: 0.7120 (ptmt) REVERT: A 674 CYS cc_start: 0.8193 (m) cc_final: 0.7487 (t) REVERT: A 678 ASP cc_start: 0.7483 (m-30) cc_final: 0.7126 (m-30) REVERT: A 710 TYR cc_start: 0.8186 (t80) cc_final: 0.7848 (t80) REVERT: A 810 LYS cc_start: 0.8367 (mttt) cc_final: 0.8142 (mtmt) REVERT: A 843 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7557 (tpp80) REVERT: A 901 GLU cc_start: 0.8431 (pt0) cc_final: 0.8199 (pm20) REVERT: A 1000 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7741 (mmmm) REVERT: A 1006 ILE cc_start: 0.7369 (mm) cc_final: 0.6965 (mt) REVERT: A 1021 ASP cc_start: 0.7806 (m-30) cc_final: 0.7560 (m-30) REVERT: A 1031 TYR cc_start: 0.8574 (m-10) cc_final: 0.8325 (m-80) REVERT: A 1071 SER cc_start: 0.8605 (t) cc_final: 0.8397 (p) REVERT: A 1072 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7959 (mmtm) REVERT: A 1096 HIS cc_start: 0.7559 (m90) cc_final: 0.7073 (m90) REVERT: A 1155 ILE cc_start: 0.8256 (mm) cc_final: 0.7867 (mm) REVERT: A 1278 LEU cc_start: 0.8139 (mt) cc_final: 0.7554 (mt) outliers start: 25 outliers final: 16 residues processed: 197 average time/residue: 0.1272 time to fit residues: 33.7995 Evaluate side-chains 196 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145368 restraints weight = 16797.163| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.37 r_work: 0.3447 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11874 Z= 0.191 Angle : 0.568 11.055 16342 Z= 0.304 Chirality : 0.043 0.320 1819 Planarity : 0.004 0.045 1861 Dihedral : 19.940 174.947 2199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.30 % Allowed : 15.70 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1238 helix: 1.94 (0.21), residues: 613 sheet: -0.70 (0.39), residues: 171 loop : 0.19 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 955 TYR 0.021 0.002 TYR A1106 PHE 0.028 0.002 PHE A1154 TRP 0.009 0.001 TRP A 958 HIS 0.007 0.001 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (11871) covalent geometry : angle 0.56822 / 0.30 (16342) hydrogen bonds : bond 0.04008 / 4.28 ( 571) hydrogen bonds : angle 4.26115 / 5.47 ( 1574) Misc. bond : bond 0.00078 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8251 (t0) cc_final: 0.7586 (t0) REVERT: A 34 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8194 (mm-40) REVERT: A 68 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6733 (pp) REVERT: A 235 THR cc_start: 0.2690 (OUTLIER) cc_final: 0.2435 (t) REVERT: A 470 GLN cc_start: 0.7452 (mt0) cc_final: 0.7098 (mp10) REVERT: A 536 GLN cc_start: 0.8213 (mp10) cc_final: 0.7907 (mp10) REVERT: A 585 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: A 604 MET cc_start: 0.8519 (mmm) cc_final: 0.8224 (mmt) REVERT: A 655 PHE cc_start: 0.7690 (m-10) cc_final: 0.7110 (m-10) REVERT: A 662 LYS cc_start: 0.7429 (ptmt) cc_final: 0.7050 (ptmt) REVERT: A 674 CYS cc_start: 0.8256 (m) cc_final: 0.7533 (t) REVERT: A 678 ASP cc_start: 0.7489 (m-30) cc_final: 0.7133 (m-30) REVERT: A 710 TYR cc_start: 0.8209 (t80) cc_final: 0.7867 (t80) REVERT: A 843 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7548 (tpp80) REVERT: A 884 SER cc_start: 0.8161 (m) cc_final: 0.7946 (m) REVERT: A 901 GLU cc_start: 0.8442 (pt0) cc_final: 0.8219 (pm20) REVERT: A 1000 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7759 (mmmm) REVERT: A 1006 ILE cc_start: 0.7413 (mm) cc_final: 0.6987 (mt) REVERT: A 1021 ASP cc_start: 0.7861 (m-30) cc_final: 0.7621 (m-30) REVERT: A 1072 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7984 (mmtm) REVERT: A 1096 HIS cc_start: 0.7541 (m90) cc_final: 0.7062 (m90) REVERT: A 1119 MET cc_start: 0.8478 (mmt) cc_final: 0.8237 (mmm) REVERT: A 1155 ILE cc_start: 0.8286 (mm) cc_final: 0.7898 (mm) REVERT: A 1278 LEU cc_start: 0.8155 (mt) cc_final: 0.7940 (mt) outliers start: 25 outliers final: 15 residues processed: 198 average time/residue: 0.1102 time to fit residues: 29.4932 Evaluate side-chains 194 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 110 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 128 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.190757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147218 restraints weight = 16736.532| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.37 r_work: 0.3480 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11874 Z= 0.124 Angle : 0.531 8.758 16342 Z= 0.286 Chirality : 0.041 0.316 1819 Planarity : 0.004 0.035 1861 Dihedral : 19.824 174.245 2199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.11 % Allowed : 15.52 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1238 helix: 2.08 (0.21), residues: 613 sheet: -0.61 (0.42), residues: 151 loop : 0.20 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1226 TYR 0.017 0.001 TYR A1106 PHE 0.023 0.001 PHE A1154 TRP 0.005 0.001 TRP A1085 HIS 0.005 0.000 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11871) covalent geometry : angle 0.53110 / 0.29 (16342) hydrogen bonds : bond 0.03647 / 3.91 ( 571) hydrogen bonds : angle 4.13450 / 5.24 ( 1574) Misc. bond : bond 0.00056 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8228 (t0) cc_final: 0.7556 (t0) REVERT: A 34 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8198 (mm-40) REVERT: A 68 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6772 (pp) REVERT: A 235 THR cc_start: 0.2726 (OUTLIER) cc_final: 0.2486 (t) REVERT: A 470 GLN cc_start: 0.7439 (mt0) cc_final: 0.7175 (mp10) REVERT: A 567 ILE cc_start: 0.8326 (pt) cc_final: 0.7906 (mt) REVERT: A 585 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: A 604 MET cc_start: 0.8463 (mmm) cc_final: 0.8154 (mmt) REVERT: A 655 PHE cc_start: 0.7637 (m-10) cc_final: 0.7032 (m-10) REVERT: A 662 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7040 (ptmt) REVERT: A 674 CYS cc_start: 0.8182 (m) cc_final: 0.7486 (t) REVERT: A 678 ASP cc_start: 0.7484 (m-30) cc_final: 0.7131 (m-30) REVERT: A 710 TYR cc_start: 0.8158 (t80) cc_final: 0.7727 (t80) REVERT: A 728 GLU cc_start: 0.7813 (tt0) cc_final: 0.7392 (tm-30) REVERT: A 843 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7512 (tpp80) REVERT: A 901 GLU cc_start: 0.8416 (pt0) cc_final: 0.8188 (pm20) REVERT: A 1000 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7737 (mmmm) REVERT: A 1021 ASP cc_start: 0.7773 (m-30) cc_final: 0.7527 (m-30) REVERT: A 1072 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7916 (mmtm) REVERT: A 1096 HIS cc_start: 0.7523 (m90) cc_final: 0.7080 (m90) REVERT: A 1107 ASP cc_start: 0.7996 (t0) cc_final: 0.7568 (t0) REVERT: A 1155 ILE cc_start: 0.8281 (mm) cc_final: 0.7908 (mm) REVERT: A 1250 ASP cc_start: 0.7280 (t70) cc_final: 0.7014 (t0) outliers start: 23 outliers final: 13 residues processed: 190 average time/residue: 0.1156 time to fit residues: 29.6411 Evaluate side-chains 192 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147163 restraints weight = 16669.908| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.15 r_work: 0.3455 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11874 Z= 0.208 Angle : 0.576 8.633 16342 Z= 0.308 Chirality : 0.044 0.326 1819 Planarity : 0.004 0.039 1861 Dihedral : 19.909 172.989 2199 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.20 % Allowed : 16.25 % Favored : 81.54 % 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: 1.41 (0.25), residues: 1238 helix: 2.00 (0.21), residues: 613 sheet: -0.62 (0.40), residues: 162 loop : 0.19 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1226 TYR 0.019 0.002 TYR A1106 PHE 0.022 0.002 PHE A1140 TRP 0.009 0.001 TRP A 958 HIS 0.005 0.001 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (11871) covalent geometry : angle 0.57645 / 0.31 (16342) hydrogen bonds : bond 0.03989 / 4.27 ( 571) hydrogen bonds : angle 4.24661 / 5.41 ( 1574) Misc. bond : bond 0.00070 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8237 (t0) cc_final: 0.7589 (t0) REVERT: A 68 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6851 (pp) REVERT: A 235 THR cc_start: 0.2748 (OUTLIER) cc_final: 0.2493 (t) REVERT: A 470 GLN cc_start: 0.7484 (mt0) cc_final: 0.7191 (mp10) REVERT: A 585 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8299 (ttpp) REVERT: A 604 MET cc_start: 0.8502 (mmm) cc_final: 0.8246 (mmt) REVERT: A 655 PHE cc_start: 0.7699 (m-10) cc_final: 0.7124 (m-10) REVERT: A 662 LYS cc_start: 0.7422 (ptmt) cc_final: 0.7061 (ptmt) REVERT: A 674 CYS cc_start: 0.8254 (m) cc_final: 0.7536 (t) REVERT: A 678 ASP cc_start: 0.7444 (m-30) cc_final: 0.7091 (m-30) REVERT: A 710 TYR cc_start: 0.8212 (t80) cc_final: 0.7858 (t80) REVERT: A 728 GLU cc_start: 0.7856 (tt0) cc_final: 0.7450 (tm-30) REVERT: A 843 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7515 (mtp-110) REVERT: A 884 SER cc_start: 0.8102 (m) cc_final: 0.7889 (m) REVERT: A 901 GLU cc_start: 0.8407 (pt0) cc_final: 0.8173 (pm20) REVERT: A 1000 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7721 (mmmm) REVERT: A 1021 ASP cc_start: 0.7848 (m-30) cc_final: 0.7597 (m-30) REVERT: A 1072 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7951 (mmtm) REVERT: A 1096 HIS cc_start: 0.7498 (m90) cc_final: 0.7074 (m90) REVERT: A 1107 ASP cc_start: 0.8000 (t0) cc_final: 0.7597 (t0) REVERT: A 1155 ILE cc_start: 0.8319 (mm) cc_final: 0.7912 (mm) REVERT: A 1250 ASP cc_start: 0.7242 (t70) cc_final: 0.6991 (t0) REVERT: A 1278 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7627 (mt) outliers start: 24 outliers final: 15 residues processed: 196 average time/residue: 0.1191 time to fit residues: 31.6137 Evaluate side-chains 199 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.0770 chunk 122 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148691 restraints weight = 16724.471| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.28 r_work: 0.3476 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11874 Z= 0.133 Angle : 0.560 8.393 16342 Z= 0.298 Chirality : 0.041 0.322 1819 Planarity : 0.004 0.039 1861 Dihedral : 19.822 173.805 2199 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.93 % Allowed : 16.53 % Favored : 81.54 % 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: 1.51 (0.25), residues: 1238 helix: 2.07 (0.21), residues: 613 sheet: -0.59 (0.41), residues: 153 loop : 0.23 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1226 TYR 0.018 0.001 TYR A 595 PHE 0.021 0.001 PHE A1154 TRP 0.005 0.001 TRP A1258 HIS 0.005 0.000 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11871) covalent geometry : angle 0.55978 / 0.30 (16342) hydrogen bonds : bond 0.03626 / 3.89 ( 571) hydrogen bonds : angle 4.13274 / 5.22 ( 1574) Misc. bond : bond 0.00056 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8187 (t0) cc_final: 0.7535 (t0) REVERT: A 68 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6819 (pp) REVERT: A 235 THR cc_start: 0.2770 (OUTLIER) cc_final: 0.2515 (t) REVERT: A 470 GLN cc_start: 0.7453 (mt0) cc_final: 0.7168 (mp10) REVERT: A 523 LYS cc_start: 0.7359 (pttp) cc_final: 0.6950 (pttp) REVERT: A 567 ILE cc_start: 0.8322 (pt) cc_final: 0.7984 (mt) REVERT: A 585 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: A 604 MET cc_start: 0.8479 (mmm) cc_final: 0.8142 (mmt) REVERT: A 655 PHE cc_start: 0.7703 (m-10) cc_final: 0.7145 (m-10) REVERT: A 662 LYS cc_start: 0.7437 (ptmt) cc_final: 0.7089 (ptmt) REVERT: A 674 CYS cc_start: 0.8188 (m) cc_final: 0.7497 (t) REVERT: A 678 ASP cc_start: 0.7418 (m-30) cc_final: 0.7069 (m-30) REVERT: A 710 TYR cc_start: 0.8162 (t80) cc_final: 0.7784 (t80) REVERT: A 728 GLU cc_start: 0.7744 (tt0) cc_final: 0.7432 (tm-30) REVERT: A 843 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7511 (mtp-110) REVERT: A 901 GLU cc_start: 0.8369 (pt0) cc_final: 0.8133 (pm20) REVERT: A 1000 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7743 (mmmm) REVERT: A 1021 ASP cc_start: 0.7773 (m-30) cc_final: 0.7519 (m-30) REVERT: A 1072 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7955 (mmtm) REVERT: A 1096 HIS cc_start: 0.7501 (m90) cc_final: 0.7067 (m90) REVERT: A 1107 ASP cc_start: 0.7995 (t0) cc_final: 0.7586 (t0) REVERT: A 1146 GLN cc_start: 0.8245 (mm110) cc_final: 0.8016 (mm-40) REVERT: A 1155 ILE cc_start: 0.8300 (mm) cc_final: 0.7897 (mm) REVERT: A 1193 PHE cc_start: 0.8821 (p90) cc_final: 0.8461 (p90) REVERT: A 1250 ASP cc_start: 0.7226 (t70) cc_final: 0.6993 (t0) outliers start: 21 outliers final: 14 residues processed: 197 average time/residue: 0.1293 time to fit residues: 34.5808 Evaluate side-chains 196 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1210 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 116 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 ASN A 784 GLN A 831 ASN A1116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.189386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144491 restraints weight = 16692.325| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.17 r_work: 0.3467 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11874 Z= 0.165 Angle : 0.576 8.638 16342 Z= 0.305 Chirality : 0.043 0.332 1819 Planarity : 0.004 0.039 1861 Dihedral : 19.836 173.550 2199 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.74 % Allowed : 17.08 % Favored : 81.18 % 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: 1.52 (0.25), residues: 1238 helix: 2.07 (0.21), residues: 613 sheet: -0.55 (0.40), residues: 163 loop : 0.26 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1226 TYR 0.018 0.002 TYR A1106 PHE 0.019 0.002 PHE A1063 TRP 0.008 0.001 TRP A 958 HIS 0.004 0.001 HIS A 977 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11871) covalent geometry : angle 0.57601 / 0.30 (16342) hydrogen bonds : bond 0.03763 / 4.02 ( 571) hydrogen bonds : angle 4.14559 / 5.25 ( 1574) Misc. bond : bond 0.00074 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.29 seconds wall clock time: 50 minutes 20.59 seconds (3020.59 seconds total)