Starting phenix.real_space_refine on Sat Jul 4 07:01:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cji_45632/07_2026/9cji_45632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cji_45632/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cji_45632/07_2026/9cji_45632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cji_45632/07_2026/9cji_45632.map" model { file = "/net/cci-nas-00/data/ceres_data/9cji_45632/07_2026/9cji_45632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cji_45632/07_2026/9cji_45632.cif" } 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-dev-6108/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: 2.89, per 1000 atoms: 0.25 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: 1.19 Conformation dependent library (CDL) restraints added in 532.9 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: 1.38 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: 2.66 Time building geometry restraints manager: 1.48 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: 15933 1.69 - 3.38: 339 3.38 - 5.07: 51 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: 1506 0.052 - 0.103: 269 0.103 - 0.155: 40 0.155 - 0.206: 2 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- 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= 0.302 Angle : 0.595 8.453 16342 Z= 0.410 Chirality : 0.041 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 0.00354 / 0.25 (11871) covalent geometry : angle 0.59514 / 0.41 (16342) hydrogen bonds : bond 0.18460 / 20.25 ( 571) hydrogen bonds : angle 6.99843 / 8.89 ( 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 : 0.454 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: 0.7325 (t0) REVERT: A 523 LYS cc_start: 0.6992 (pttp) cc_final: 0.6612 (pttp) REVERT: A 528 VAL cc_start: 0.7809 (t) cc_final: 0.7513 (t) REVERT: A 568 MET cc_start: 0.7740 (mpp) cc_final: 0.7252 (mtm) REVERT: A 594 TYR cc_start: 0.8179 (m-80) cc_final: 0.7929 (m-80) 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: 0.7605 (mm) REVERT: A 674 CYS cc_start: 0.7245 (m) cc_final: 0.6906 (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: 0.7422 (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: 0.7302 (mm-40) REVERT: A 843 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.7040 (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: 0.8002 (p) REVERT: A 860 LYS cc_start: 0.8052 (tttp) cc_final: 0.7681 (tttm) REVERT: A 1006 ILE cc_start: 0.7583 (mm) cc_final: 0.7289 (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: 0.7327 (mmtm) REVERT: A 1096 HIS cc_start: 0.6336 (m90) cc_final: 0.6040 (m90) REVERT: A 1116 HIS cc_start: 0.7201 (t70) cc_final: 0.7001 (t-90) REVERT: A 1141 GLU cc_start: 0.6517 (mm-30) cc_final: 0.5059 (mm-30) REVERT: A 1142 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7587 (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: 0.6657 (mtt-85) REVERT: A 1279 ASN cc_start: 0.7944 (m-40) cc_final: 0.7743 (m-40) outliers start: 9 outliers final: 2 residues processed: 206 average time/residue: 0.1446 time to fit residues: 40.1017 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 : 0.403 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.192759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150084 restraints weight = 16907.684| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.35 r_work: 0.3451 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11874 Z= 0.183 Angle : 0.608 8.478 16342 Z= 0.325 Chirality : 0.044 0.262 1819 Planarity : 0.004 0.036 1861 Dihedral : 20.155 178.608 2204 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.74 % Allowed : 8.82 % Favored : 89.44 % 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: 0.82 (0.25), residues: 1238 helix: 1.28 (0.21), residues: 597 sheet: -0.46 (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 0.041 0.002 PHE A 165 TRP 0.014 0.002 TRP A 958 HIS 0.009 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (11871) covalent geometry : angle 0.60804 / 0.33 (16342) hydrogen bonds : bond 0.04976 / 5.49 ( 571) hydrogen bonds : angle 4.96126 / 6.19 ( 1574) Misc. bond : bond 0.00857 / 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 198 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8143 (t0) cc_final: 0.7589 (t0) REVERT: A 34 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 523 LYS cc_start: 0.7306 (pttp) cc_final: 0.6954 (pttp) REVERT: A 536 GLN cc_start: 0.8036 (mp10) cc_final: 0.7736 (mp10) REVERT: A 550 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8112 (tmtt) REVERT: A 594 TYR cc_start: 0.8467 (m-80) cc_final: 0.8181 (m-80) REVERT: A 600 ASP cc_start: 0.7166 (t0) cc_final: 0.6891 (t70) REVERT: A 655 PHE cc_start: 0.7621 (m-10) cc_final: 0.7006 (m-10) REVERT: A 674 CYS cc_start: 0.7994 (m) cc_final: 0.7220 (t) REVERT: A 678 ASP cc_start: 0.7276 (m-30) cc_final: 0.6875 (m-30) REVERT: A 736 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 757 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7789 (mtmm) REVERT: A 772 GLU cc_start: 0.7308 (pm20) cc_final: 0.7097 (pm20) REVERT: A 806 MET cc_start: 0.7459 (mtp) cc_final: 0.7122 (mtm) REVERT: A 843 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7436 (tpp80) REVERT: A 848 ASN cc_start: 0.7704 (t0) cc_final: 0.7339 (t0) REVERT: A 854 VAL cc_start: 0.8523 (t) cc_final: 0.8120 (p) REVERT: A 897 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8069 (mtpp) REVERT: A 901 GLU cc_start: 0.8319 (pt0) cc_final: 0.8050 (pm20) REVERT: A 911 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7303 (mp0) REVERT: A 1006 ILE cc_start: 0.7446 (mm) cc_final: 0.7206 (mm) REVERT: A 1021 ASP cc_start: 0.7659 (m-30) cc_final: 0.7411 (m-30) REVERT: A 1031 TYR cc_start: 0.8484 (m-10) cc_final: 0.8094 (m-80) REVERT: A 1069 TYR cc_start: 0.8144 (m-80) cc_final: 0.7851 (m-80) REVERT: A 1071 SER cc_start: 0.8581 (t) cc_final: 0.8263 (p) REVERT: A 1072 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7560 (mmtm) REVERT: A 1096 HIS cc_start: 0.7284 (m90) cc_final: 0.6942 (m90) REVERT: A 1141 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6765 (mm-30) REVERT: A 1142 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7916 (ttpp) REVERT: A 1242 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7313 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7214 (t0) cc_final: 0.6976 (t0) REVERT: A 1279 ASN cc_start: 0.8081 (m-40) cc_final: 0.7880 (m-40) outliers start: 19 outliers final: 7 residues processed: 188 average time/residue: 0.1305 time to fit residues: 33.2340 Evaluate side-chains 175 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 39 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.192009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149494 restraints weight = 16946.910| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.27 r_work: 0.3420 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11874 Z= 0.157 Angle : 0.549 7.502 16342 Z= 0.297 Chirality : 0.042 0.257 1819 Planarity : 0.004 0.044 1861 Dihedral : 20.130 178.865 2202 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.93 % Allowed : 11.94 % Favored : 86.13 % 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: 1.19 (0.25), residues: 1238 helix: 1.76 (0.21), residues: 599 sheet: -0.42 (0.42), residues: 153 loop : 0.09 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1226 TYR 0.014 0.002 TYR A 789 PHE 0.024 0.001 PHE A 165 TRP 0.008 0.001 TRP A 958 HIS 0.011 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (11871) covalent geometry : angle 0.54922 / 0.30 (16342) hydrogen bonds : bond 0.04327 / 4.68 ( 571) hydrogen bonds : angle 4.55165 / 5.70 ( 1574) Misc. bond : bond 0.00303 / 0.30 ( 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 195 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8289 (t0) cc_final: 0.7650 (t0) REVERT: A 34 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 470 GLN cc_start: 0.7088 (mt0) cc_final: 0.6839 (mp10) REVERT: A 536 GLN cc_start: 0.8214 (mp10) cc_final: 0.7818 (mp10) REVERT: A 550 LYS cc_start: 0.8670 (tmtt) cc_final: 0.8167 (tmtt) REVERT: A 585 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8114 (ttpp) REVERT: A 655 PHE cc_start: 0.7747 (m-10) cc_final: 0.7129 (m-10) REVERT: A 674 CYS cc_start: 0.8194 (m) cc_final: 0.7440 (t) REVERT: A 678 ASP cc_start: 0.7529 (m-30) cc_final: 0.7136 (m-30) REVERT: A 757 LYS cc_start: 0.8123 (ptpp) cc_final: 0.7870 (mtmm) REVERT: A 806 MET cc_start: 0.7721 (mtp) cc_final: 0.7472 (mtm) REVERT: A 810 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7960 (mtpt) REVERT: A 843 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7549 (tpp80) REVERT: A 848 ASN cc_start: 0.7887 (t0) cc_final: 0.7498 (t0) REVERT: A 854 VAL cc_start: 0.8584 (t) cc_final: 0.8186 (p) REVERT: A 901 GLU cc_start: 0.8493 (pt0) cc_final: 0.8230 (pm20) REVERT: A 1006 ILE cc_start: 0.7504 (mm) cc_final: 0.6752 (mt) REVERT: A 1021 ASP cc_start: 0.7747 (m-30) cc_final: 0.7520 (m-30) REVERT: A 1031 TYR cc_start: 0.8583 (m-10) cc_final: 0.8206 (m-80) REVERT: A 1071 SER cc_start: 0.8631 (t) cc_final: 0.8387 (p) REVERT: A 1072 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7860 (mmtm) REVERT: A 1096 HIS cc_start: 0.7516 (m90) cc_final: 0.7070 (m90) REVERT: A 1142 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8156 (ttpp) REVERT: A 1242 ARG cc_start: 0.7718 (mtt-85) cc_final: 0.7455 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7383 (t0) cc_final: 0.7155 (t70) outliers start: 21 outliers final: 11 residues processed: 185 average time/residue: 0.1378 time to fit residues: 34.3175 Evaluate side-chains 181 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 585 LYS Chi-restraints excluded: chain A residue 729 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 1001 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: 3.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.189429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147922 restraints weight = 16869.953| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.09 r_work: 0.3451 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11874 Z= 0.242 Angle : 0.602 8.576 16342 Z= 0.323 Chirality : 0.045 0.273 1819 Planarity : 0.004 0.061 1861 Dihedral : 20.239 179.941 2199 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.48 % Allowed : 12.95 % Favored : 84.57 % 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: 1.14 (0.25), residues: 1238 helix: 1.77 (0.22), residues: 605 sheet: -0.52 (0.41), residues: 165 loop : 0.01 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 862 TYR 0.018 0.002 TYR A1268 PHE 0.021 0.002 PHE A 165 TRP 0.014 0.002 TRP A 958 HIS 0.015 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (11871) covalent geometry : angle 0.60232 / 0.32 (16342) hydrogen bonds : bond 0.04504 / 4.80 ( 571) hydrogen bonds : angle 4.52271 / 5.70 ( 1574) Misc. bond : bond 0.00309 / 0.28 ( 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 209 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.428 Fit side-chains REVERT: A 5 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8110 (mm-30) REVERT: A 9 ASN cc_start: 0.8302 (t0) cc_final: 0.7654 (t0) REVERT: A 32 GLN cc_start: 0.8385 (mt0) cc_final: 0.8165 (mt0) REVERT: A 34 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8229 (mm-40) REVERT: A 470 GLN cc_start: 0.7282 (mt0) cc_final: 0.6972 (mp10) REVERT: A 523 LYS cc_start: 0.7362 (pttp) cc_final: 0.6991 (pttp) REVERT: A 536 GLN cc_start: 0.8240 (mp10) cc_final: 0.7971 (mp10) REVERT: A 585 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: A 604 MET cc_start: 0.8596 (mmm) cc_final: 0.8339 (mmt) REVERT: A 655 PHE cc_start: 0.7770 (m-10) cc_final: 0.7189 (m-10) REVERT: A 674 CYS cc_start: 0.8302 (m) cc_final: 0.7530 (t) REVERT: A 678 ASP cc_start: 0.7453 (m-30) cc_final: 0.7088 (m-30) REVERT: A 843 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7584 (tpp80) REVERT: A 854 VAL cc_start: 0.8676 (t) cc_final: 0.8375 (p) REVERT: A 901 GLU cc_start: 0.8490 (pt0) cc_final: 0.8260 (pm20) REVERT: A 955 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7452 (mtp180) REVERT: A 1021 ASP cc_start: 0.7835 (m-30) cc_final: 0.7599 (m-30) REVERT: A 1071 SER cc_start: 0.8621 (t) cc_final: 0.8356 (p) REVERT: A 1072 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7907 (mmtm) REVERT: A 1074 ASP cc_start: 0.8450 (t0) cc_final: 0.7815 (t0) REVERT: A 1096 HIS cc_start: 0.7533 (m90) cc_final: 0.7124 (m90) REVERT: A 1155 ILE cc_start: 0.8306 (mm) cc_final: 0.7816 (mm) REVERT: A 1250 ASP cc_start: 0.7382 (t0) cc_final: 0.7118 (t70) outliers start: 27 outliers final: 18 residues processed: 197 average time/residue: 0.1424 time to fit residues: 37.9199 Evaluate side-chains 191 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU 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 636 LEU Chi-restraints excluded: chain A residue 766 THR 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 886 SER Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1001 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 878 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146597 restraints weight = 16838.054| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.44 r_work: 0.3452 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11874 Z= 0.159 Angle : 0.542 6.897 16342 Z= 0.295 Chirality : 0.043 0.268 1819 Planarity : 0.004 0.058 1861 Dihedral : 20.158 178.290 2199 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.74 % Allowed : 15.15 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1238 helix: 1.94 (0.21), residues: 606 sheet: -0.63 (0.40), residues: 163 loop : 0.08 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1226 TYR 0.016 0.001 TYR A 595 PHE 0.027 0.001 PHE A1154 TRP 0.007 0.001 TRP A 958 HIS 0.013 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11871) covalent geometry : angle 0.54222 / 0.30 (16342) hydrogen bonds : bond 0.03989 / 4.25 ( 571) hydrogen bonds : angle 4.33221 / 5.45 ( 1574) Misc. bond : bond 0.00090 / 0.06 ( 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 200 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8041 (t0) cc_final: 0.7383 (t0) REVERT: A 32 GLN cc_start: 0.8257 (mt0) cc_final: 0.8050 (mt0) REVERT: A 34 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8068 (mm-40) REVERT: A 235 THR cc_start: 0.2679 (OUTLIER) cc_final: 0.2443 (t) REVERT: A 470 GLN cc_start: 0.7091 (mt0) cc_final: 0.6733 (mp10) REVERT: A 536 GLN cc_start: 0.8074 (mp10) cc_final: 0.7790 (mp10) REVERT: A 558 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (t) REVERT: A 585 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (ttpp) REVERT: A 604 MET cc_start: 0.8361 (mmm) cc_final: 0.8050 (mmt) REVERT: A 655 PHE cc_start: 0.7598 (m-10) cc_final: 0.7008 (m-10) REVERT: A 662 LYS cc_start: 0.7433 (ptmt) cc_final: 0.7062 (ptmt) REVERT: A 674 CYS cc_start: 0.7984 (m) cc_final: 0.7244 (t) REVERT: A 678 ASP cc_start: 0.7312 (m-30) cc_final: 0.6940 (m-30) REVERT: A 710 TYR cc_start: 0.8026 (t80) cc_final: 0.7701 (t80) REVERT: A 843 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7365 (tpp80) REVERT: A 901 GLU cc_start: 0.8263 (pt0) cc_final: 0.8026 (pm20) REVERT: A 955 ARG cc_start: 0.7270 (mtp180) cc_final: 0.7031 (mtp180) REVERT: A 993 GLU cc_start: 0.7437 (pm20) cc_final: 0.7088 (pt0) REVERT: A 1006 ILE cc_start: 0.7296 (mm) cc_final: 0.6805 (mt) REVERT: A 1021 ASP cc_start: 0.7639 (m-30) cc_final: 0.7394 (m-30) REVERT: A 1031 TYR cc_start: 0.8499 (m-10) cc_final: 0.8231 (m-80) REVERT: A 1071 SER cc_start: 0.8543 (t) cc_final: 0.8254 (p) REVERT: A 1072 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7770 (mmtm) REVERT: A 1096 HIS cc_start: 0.7203 (m90) cc_final: 0.6788 (m90) REVERT: A 1250 ASP cc_start: 0.7215 (t0) cc_final: 0.6907 (t0) outliers start: 19 outliers final: 10 residues processed: 191 average time/residue: 0.1428 time to fit residues: 36.7593 Evaluate side-chains 189 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 1001 SER Chi-restraints excluded: chain A residue 1036 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: 2.9990 chunk 110 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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 = 0.4223 r_free = 0.4223 target = 0.189526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146172 restraints weight = 16867.294| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.37 r_work: 0.3383 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2627 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= 0.184 Angle : 0.563 7.661 16342 Z= 0.303 Chirality : 0.043 0.279 1819 Planarity : 0.004 0.035 1861 Dihedral : 20.105 177.537 2199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.11 % Allowed : 15.79 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1238 helix: 1.88 (0.21), residues: 612 sheet: -0.67 (0.42), residues: 153 loop : 0.09 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.020 0.002 TYR A 109 PHE 0.024 0.001 PHE A1154 TRP 0.008 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (11871) covalent geometry : angle 0.56319 / 0.30 (16342) hydrogen bonds : bond 0.04088 / 4.32 ( 571) hydrogen bonds : angle 4.32886 / 5.46 ( 1574) Misc. bond : bond 0.00110 / 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 202 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8041 (t0) cc_final: 0.7370 (t0) REVERT: A 32 GLN cc_start: 0.8265 (mt0) cc_final: 0.8045 (mt0) REVERT: A 34 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 68 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6609 (pp) REVERT: A 470 GLN cc_start: 0.7185 (mt0) cc_final: 0.6838 (mp10) REVERT: A 536 GLN cc_start: 0.8087 (mp10) cc_final: 0.7787 (mp10) REVERT: A 585 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: A 604 MET cc_start: 0.8345 (mmm) cc_final: 0.8065 (mmt) REVERT: A 655 PHE cc_start: 0.7553 (m-10) cc_final: 0.6996 (m-10) REVERT: A 662 LYS cc_start: 0.7456 (ptmt) cc_final: 0.7075 (ptmt) REVERT: A 674 CYS cc_start: 0.7938 (m) cc_final: 0.7245 (t) REVERT: A 678 ASP cc_start: 0.7274 (m-30) cc_final: 0.6907 (m-30) REVERT: A 710 TYR cc_start: 0.8055 (t80) cc_final: 0.7739 (t80) REVERT: A 843 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7380 (tpp80) REVERT: A 860 LYS cc_start: 0.8057 (tttm) cc_final: 0.7826 (tttm) REVERT: A 901 GLU cc_start: 0.8244 (pt0) cc_final: 0.8014 (pm20) REVERT: A 955 ARG cc_start: 0.7308 (mtp180) cc_final: 0.7092 (mtp180) REVERT: A 1006 ILE cc_start: 0.7320 (mm) cc_final: 0.6811 (mt) REVERT: A 1021 ASP cc_start: 0.7655 (m-30) cc_final: 0.7408 (m-30) REVERT: A 1031 TYR cc_start: 0.8479 (m-10) cc_final: 0.8264 (m-80) REVERT: A 1071 SER cc_start: 0.8531 (t) cc_final: 0.8314 (p) REVERT: A 1072 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7771 (mmtm) REVERT: A 1096 HIS cc_start: 0.7226 (m90) cc_final: 0.6807 (m90) REVERT: A 1155 ILE cc_start: 0.8197 (mm) cc_final: 0.7838 (mm) REVERT: A 1250 ASP cc_start: 0.7198 (t0) cc_final: 0.6866 (t0) outliers start: 23 outliers final: 15 residues processed: 193 average time/residue: 0.1421 time to fit residues: 36.9288 Evaluate side-chains 192 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 867 ASP Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1041 ASN 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: 9.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 79 optimal weight: 0.0270 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- 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 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 = 0.4220 r_free = 0.4220 target = 0.189084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145469 restraints weight = 16781.713| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.44 r_work: 0.3439 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2802 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= 0.179 Angle : 0.561 8.625 16342 Z= 0.303 Chirality : 0.044 0.293 1819 Planarity : 0.004 0.067 1861 Dihedral : 19.991 176.216 2199 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 15.89 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1238 helix: 1.90 (0.21), residues: 613 sheet: -0.74 (0.41), residues: 161 loop : 0.15 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1226 TYR 0.017 0.002 TYR A 595 PHE 0.022 0.001 PHE A1154 TRP 0.008 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (11871) covalent geometry : angle 0.56147 / 0.30 (16342) hydrogen bonds : bond 0.03985 / 4.21 ( 571) hydrogen bonds : angle 4.27110 / 5.35 ( 1574) Misc. bond : bond 0.00100 / 0.06 ( 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: 27 poor density : 179 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8016 (t0) cc_final: 0.7353 (t0) REVERT: A 32 GLN cc_start: 0.8269 (mt0) cc_final: 0.8004 (mt0) REVERT: A 34 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8054 (mm-40) REVERT: A 68 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6784 (pp) REVERT: A 235 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.2459 (t) REVERT: A 470 GLN cc_start: 0.7247 (mt0) cc_final: 0.6878 (mp10) REVERT: A 523 LYS cc_start: 0.7243 (pttp) cc_final: 0.6863 (pttp) REVERT: A 536 GLN cc_start: 0.8067 (mp10) cc_final: 0.7753 (mp10) REVERT: A 585 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8207 (ttpp) REVERT: A 604 MET cc_start: 0.8333 (mmm) cc_final: 0.8051 (mmt) REVERT: A 655 PHE cc_start: 0.7540 (m-10) cc_final: 0.6955 (m-10) REVERT: A 662 LYS cc_start: 0.7350 (ptmt) cc_final: 0.6987 (ptmt) REVERT: A 674 CYS cc_start: 0.7994 (m) cc_final: 0.7294 (t) REVERT: A 678 ASP cc_start: 0.7293 (m-30) cc_final: 0.6931 (m-30) REVERT: A 710 TYR cc_start: 0.8066 (t80) cc_final: 0.7755 (t80) REVERT: A 843 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7417 (tpp80) REVERT: A 901 GLU cc_start: 0.8265 (pt0) cc_final: 0.8024 (pm20) REVERT: A 955 ARG cc_start: 0.7421 (mtp180) cc_final: 0.7196 (mtp180) REVERT: A 1006 ILE cc_start: 0.7284 (mm) cc_final: 0.6783 (mt) REVERT: A 1021 ASP cc_start: 0.7659 (m-30) cc_final: 0.7405 (m-30) REVERT: A 1071 SER cc_start: 0.8540 (t) cc_final: 0.8320 (p) REVERT: A 1072 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7816 (mmtm) REVERT: A 1096 HIS cc_start: 0.7181 (m90) cc_final: 0.6786 (m90) REVERT: A 1155 ILE cc_start: 0.8234 (mm) cc_final: 0.7874 (mm) REVERT: A 1242 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7333 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7162 (t0) cc_final: 0.6879 (t0) REVERT: A 1278 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 27 outliers final: 15 residues processed: 196 average time/residue: 0.1351 time to fit residues: 35.9783 Evaluate side-chains 194 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1001 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 560 ASN A 784 GLN 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 = 0.4228 r_free = 0.4228 target = 0.190065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145789 restraints weight = 16662.160| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.16 r_work: 0.3471 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11874 Z= 0.153 Angle : 0.550 8.847 16342 Z= 0.296 Chirality : 0.042 0.294 1819 Planarity : 0.004 0.048 1861 Dihedral : 19.923 175.306 2199 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.75 % Allowed : 15.34 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1238 helix: 2.00 (0.21), residues: 613 sheet: -0.62 (0.42), residues: 151 loop : 0.14 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.021 0.002 TYR A1106 PHE 0.021 0.001 PHE A1154 TRP 0.007 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11871) covalent geometry : angle 0.55038 / 0.30 (16342) hydrogen bonds : bond 0.03827 / 4.04 ( 571) hydrogen bonds : angle 4.21091 / 5.25 ( 1574) Misc. bond : bond 0.00063 / 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 211 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8203 (t0) cc_final: 0.7545 (t0) REVERT: A 32 GLN cc_start: 0.8410 (mt0) cc_final: 0.8142 (mt0) REVERT: A 68 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6788 (pp) REVERT: A 235 THR cc_start: 0.2748 (OUTLIER) cc_final: 0.2502 (t) REVERT: A 470 GLN cc_start: 0.7447 (mt0) cc_final: 0.7173 (mp10) REVERT: A 523 LYS cc_start: 0.7305 (pttp) cc_final: 0.6899 (pttp) REVERT: A 536 GLN cc_start: 0.8191 (mp10) cc_final: 0.7918 (mp10) REVERT: A 585 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8283 (ttpp) REVERT: A 604 MET cc_start: 0.8480 (mmm) cc_final: 0.8172 (mmt) REVERT: A 655 PHE cc_start: 0.7667 (m-10) cc_final: 0.7135 (m-10) REVERT: A 662 LYS cc_start: 0.7415 (ptmt) cc_final: 0.7051 (ptmt) REVERT: A 674 CYS cc_start: 0.8194 (m) cc_final: 0.7497 (t) REVERT: A 678 ASP cc_start: 0.7438 (m-30) cc_final: 0.7090 (m-30) REVERT: A 710 TYR cc_start: 0.8176 (t80) cc_final: 0.7817 (t80) REVERT: A 843 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7563 (tpp80) REVERT: A 901 GLU cc_start: 0.8428 (pt0) cc_final: 0.8193 (pm20) REVERT: A 955 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7449 (mtp180) REVERT: A 1021 ASP cc_start: 0.7781 (m-30) cc_final: 0.7535 (m-30) REVERT: A 1072 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7963 (mmtm) REVERT: A 1096 HIS cc_start: 0.7490 (m90) cc_final: 0.7069 (m90) REVERT: A 1107 ASP cc_start: 0.7975 (t0) cc_final: 0.7561 (t0) REVERT: A 1141 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 1155 ILE cc_start: 0.8295 (mm) cc_final: 0.7940 (mm) REVERT: A 1242 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7445 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7333 (t0) cc_final: 0.7051 (t70) REVERT: A 1278 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7650 (mt) outliers start: 30 outliers final: 18 residues processed: 198 average time/residue: 0.1397 time to fit residues: 37.5263 Evaluate side-chains 198 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 809 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1001 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A 831 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146189 restraints weight = 16580.999| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.19 r_work: 0.3470 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11874 Z= 0.156 Angle : 0.552 8.959 16342 Z= 0.296 Chirality : 0.042 0.299 1819 Planarity : 0.004 0.075 1861 Dihedral : 19.893 174.600 2199 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.30 % Allowed : 16.71 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1238 helix: 2.06 (0.21), residues: 613 sheet: -0.60 (0.42), residues: 151 loop : 0.14 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1226 TYR 0.019 0.001 TYR A1106 PHE 0.020 0.001 PHE A1154 TRP 0.007 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (11871) covalent geometry : angle 0.55227 / 0.30 (16342) hydrogen bonds : bond 0.03785 / 3.99 ( 571) hydrogen bonds : angle 4.18569 / 5.22 ( 1574) Misc. bond : bond 0.00061 / 0.03 ( 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 208 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8201 (t0) cc_final: 0.7542 (t0) REVERT: A 32 GLN cc_start: 0.8410 (mt0) cc_final: 0.8148 (mt0) REVERT: A 43 ARG cc_start: 0.6507 (tmt170) cc_final: 0.5746 (ttm170) REVERT: A 68 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6743 (pp) REVERT: A 235 THR cc_start: 0.2779 (OUTLIER) cc_final: 0.2533 (t) REVERT: A 470 GLN cc_start: 0.7456 (mt0) cc_final: 0.7170 (mp10) REVERT: A 523 LYS cc_start: 0.7301 (pttp) cc_final: 0.6870 (pttp) REVERT: A 536 GLN cc_start: 0.8207 (mp10) cc_final: 0.7946 (mp10) REVERT: A 585 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: A 604 MET cc_start: 0.8475 (mmm) cc_final: 0.8188 (mmt) REVERT: A 655 PHE cc_start: 0.7748 (m-10) cc_final: 0.7181 (m-10) REVERT: A 662 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7051 (ptmt) REVERT: A 674 CYS cc_start: 0.8220 (m) cc_final: 0.7512 (t) REVERT: A 678 ASP cc_start: 0.7445 (m-30) cc_final: 0.7092 (m-30) REVERT: A 710 TYR cc_start: 0.8167 (t80) cc_final: 0.7812 (t80) REVERT: A 810 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7981 (mtpt) REVERT: A 843 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7563 (tpp80) REVERT: A 901 GLU cc_start: 0.8398 (pt0) cc_final: 0.8170 (pm20) REVERT: A 955 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7470 (mtp180) REVERT: A 1021 ASP cc_start: 0.7812 (m-30) cc_final: 0.7570 (m-30) REVERT: A 1072 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7940 (mmtm) REVERT: A 1096 HIS cc_start: 0.7485 (m90) cc_final: 0.7053 (m90) REVERT: A 1107 ASP cc_start: 0.7990 (t0) cc_final: 0.7570 (t0) REVERT: A 1155 ILE cc_start: 0.8302 (mm) cc_final: 0.7914 (mm) REVERT: A 1193 PHE cc_start: 0.8856 (p90) cc_final: 0.8496 (p90) REVERT: A 1250 ASP cc_start: 0.7343 (t0) cc_final: 0.7065 (t0) REVERT: A 1278 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7660 (mt) outliers start: 25 outliers final: 16 residues processed: 200 average time/residue: 0.1340 time to fit residues: 36.3762 Evaluate side-chains 201 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 960 VAL Chi-restraints excluded: chain A residue 1001 SER 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: 3.9990 chunk 17 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A 831 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147576 restraints weight = 16625.620| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.12 r_work: 0.3484 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11874 Z= 0.140 Angle : 0.548 9.062 16342 Z= 0.294 Chirality : 0.042 0.303 1819 Planarity : 0.004 0.054 1861 Dihedral : 19.841 174.966 2199 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.74 % Allowed : 17.26 % Favored : 80.99 % 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: 2.13 (0.21), residues: 613 sheet: -0.64 (0.40), residues: 163 loop : 0.21 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1226 TYR 0.019 0.001 TYR A1106 PHE 0.020 0.001 PHE A1154 TRP 0.006 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11871) covalent geometry : angle 0.54834 / 0.29 (16342) hydrogen bonds : bond 0.03671 / 3.86 ( 571) hydrogen bonds : angle 4.12758 / 5.12 ( 1574) Misc. bond : bond 0.00060 / 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: 19 poor density : 186 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8151 (t0) cc_final: 0.7487 (t0) REVERT: A 32 GLN cc_start: 0.8398 (mt0) cc_final: 0.8120 (mt0) REVERT: A 68 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6764 (pp) REVERT: A 235 THR cc_start: 0.2786 (OUTLIER) cc_final: 0.2528 (t) REVERT: A 470 GLN cc_start: 0.7455 (mt0) cc_final: 0.7147 (mp10) REVERT: A 523 LYS cc_start: 0.7369 (pttp) cc_final: 0.6959 (pttp) REVERT: A 536 GLN cc_start: 0.8170 (mp10) cc_final: 0.7933 (mp10) REVERT: A 567 ILE cc_start: 0.8352 (pt) cc_final: 0.7965 (mt) REVERT: A 585 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: A 604 MET cc_start: 0.8482 (mmm) cc_final: 0.8157 (mmt) REVERT: A 655 PHE cc_start: 0.7706 (m-10) cc_final: 0.7122 (m-10) REVERT: A 662 LYS cc_start: 0.7415 (ptmt) cc_final: 0.7065 (ptmt) REVERT: A 674 CYS cc_start: 0.8160 (m) cc_final: 0.7457 (t) REVERT: A 678 ASP cc_start: 0.7414 (m-30) cc_final: 0.7061 (m-30) REVERT: A 710 TYR cc_start: 0.8155 (t80) cc_final: 0.7791 (t80) REVERT: A 810 LYS cc_start: 0.8263 (mtmt) cc_final: 0.8006 (mtpt) REVERT: A 843 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7472 (mtp85) REVERT: A 901 GLU cc_start: 0.8406 (pt0) cc_final: 0.8183 (pm20) REVERT: A 955 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7549 (mtp180) REVERT: A 1000 LYS cc_start: 0.8366 (tppp) cc_final: 0.8010 (mmmm) REVERT: A 1021 ASP cc_start: 0.7771 (m-30) cc_final: 0.7521 (m-30) REVERT: A 1072 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7922 (mmtm) REVERT: A 1096 HIS cc_start: 0.7441 (m90) cc_final: 0.7036 (m90) REVERT: A 1107 ASP cc_start: 0.7982 (t0) cc_final: 0.7575 (t0) REVERT: A 1155 ILE cc_start: 0.8311 (mm) cc_final: 0.7903 (mm) REVERT: A 1193 PHE cc_start: 0.8830 (p90) cc_final: 0.8456 (p90) REVERT: A 1242 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7447 (mtt-85) REVERT: A 1250 ASP cc_start: 0.7294 (t0) cc_final: 0.7031 (t70) REVERT: A 1278 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7672 (mt) outliers start: 19 outliers final: 15 residues processed: 198 average time/residue: 0.1386 time to fit residues: 37.0887 Evaluate side-chains 200 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 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 34 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 784 GLN A 831 ASN A1105 HIS A1116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.189675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147554 restraints weight = 16681.317| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.28 r_work: 0.3448 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3136 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= 0.181 Angle : 0.572 9.636 16342 Z= 0.304 Chirality : 0.043 0.311 1819 Planarity : 0.004 0.070 1861 Dihedral : 19.867 174.294 2199 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 17.45 % Favored : 80.62 % 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: 1.48 (0.25), residues: 1238 helix: 2.09 (0.21), residues: 613 sheet: -0.60 (0.40), residues: 163 loop : 0.18 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1226 TYR 0.019 0.002 TYR A1106 PHE 0.019 0.001 PHE A1154 TRP 0.008 0.001 TRP A 958 HIS 0.012 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (11871) covalent geometry : angle 0.57250 / 0.30 (16342) hydrogen bonds : bond 0.03826 / 4.01 ( 571) hydrogen bonds : angle 4.17055 / 5.20 ( 1574) Misc. bond : bond 0.00080 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.10 seconds wall clock time: 57 minutes 4.39 seconds (3424.39 seconds total)