Starting phenix.real_space_refine on Fri Aug 7 02:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjh_45631/08_2026/9cjh_45631.map" } resolution = 3.6 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 9382 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 57 5.49 5 S 27 5.16 5 C 6976 2.51 5 N 1910 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11200 Number of models: 1 Model: "" Number of chains: 5 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: "A" Number of atoms: 10013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 10013 Classifications: {'peptide': 1236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 47, 'TRANS': 1188} Chain breaks: 4 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 Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11200 At special positions: 0 Unit cell: (98.12, 107.04, 139.375, 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 57 15.00 O 2230 8.00 N 1910 7.00 C 6976 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: 1.09 Conformation dependent library (CDL) restraints added in 510.4 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 55.0% alpha, 10.8% beta 16 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 49 through 68 removed outlier: 4.248A pdb=" N ILE A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.064A 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: 3.603A 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: 3.529A pdb=" N ASP A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.786A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.235A 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: 4.069A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.978A 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: 3.728A 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: 5.484A 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: 3.658A 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 523 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 609 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 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 694 through 698 removed outlier: 3.713A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.635A pdb=" N TYR A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Proline residue: A 716 - end of helix removed outlier: 3.895A 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: 3.622A 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 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 847 through 849 No H-bonds generated for 'chain 'A' and resid 847 through 849' Processing helix chain 'A' and resid 861 through 865 removed outlier: 3.785A pdb=" N PHE A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 943 through 955 Processing helix chain 'A' and resid 958 through 987 removed outlier: 3.709A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.509A pdb=" N LYS A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 4.046A pdb=" N PHE A1101 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1207 Processing helix chain 'A' and resid 1208 through 1224 removed outlier: 3.533A pdb=" N VAL A1216 " --> pdb=" O ILE A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.520A pdb=" N GLY A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) 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: 4.158A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.696A 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: 3.594A 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 807 Processing sheet with id=AA8, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.750A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 8.774A 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: 3.993A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) removed outlier: 3.588A 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 509 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2191 1.33 - 1.45: 3034 1.45 - 1.57: 6186 1.57 - 1.69: 111 1.69 - 1.81: 44 Bond restraints: 11566 Sorted by residual: bond pdb=" O5' 2YR C 7 " pdb=" P 2YR C 7 " ideal model delta sigma weight residual 1.721 1.599 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" N ILE A 626 " pdb=" CA ILE A 626 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.29e-02 6.01e+03 9.99e+00 bond pdb=" CB PRO A 700 " pdb=" CG PRO A 700 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.07e+00 bond pdb=" C3' DC D 21 " pdb=" C2' DC D 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" C3' DA D 22 " pdb=" C2' DA D 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.02e+00 ... (remaining 11561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 15714 2.53 - 5.06: 162 5.06 - 7.59: 7 7.59 - 10.12: 2 10.12 - 12.65: 1 Bond angle restraints: 15886 Sorted by residual: angle pdb=" CA PRO A 700 " pdb=" N PRO A 700 " pdb=" CD PRO A 700 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.16e+01 angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 113.50 104.52 8.98 1.23e+00 6.61e-01 5.33e+01 angle pdb=" O GLU A 634 " pdb=" C GLU A 634 " pdb=" N PRO A 635 " ideal model delta sigma weight residual 121.80 117.60 4.20 8.60e-01 1.35e+00 2.39e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4 DT C 10 " pdb=" C4 DT C 10 " pdb=" C5 DT C 10 " ideal model delta sigma weight residual 124.90 121.92 2.98 7.00e-01 2.04e+00 1.82e+01 ... (remaining 15881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 6510 33.55 - 67.10: 356 67.10 - 100.65: 32 100.65 - 134.20: 1 134.20 - 167.75: 2 Dihedral angle restraints: 6901 sinusoidal: 3251 harmonic: 3650 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 64.25 167.75 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" C4' DA D 24 " pdb=" C3' DA D 24 " pdb=" O3' DA D 24 " pdb=" P DG D 25 " ideal model delta sinusoidal sigma weight residual 220.00 61.57 158.43 1 3.50e+01 8.16e-04 1.51e+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 -161.28 -18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 6898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1490 0.055 - 0.110: 229 0.110 - 0.166: 48 0.166 - 0.221: 4 0.221 - 0.276: 1 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA LEU A 636 " pdb=" N LEU A 636 " pdb=" C LEU A 636 " pdb=" CB LEU A 636 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1' 2YR C 7 " pdb=" C2' 2YR C 7 " pdb=" N1 2YR C 7 " pdb=" O4' 2YR C 7 " both_signs ideal model delta sigma weight residual False 2.24 2.47 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 627 " pdb=" N LEU A 627 " pdb=" C LEU A 627 " pdb=" CB LEU A 627 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 1769 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2YR C 7 " -0.243 2.00e-02 2.50e+03 3.00e-01 2.24e+03 pdb=" C2 2YR C 7 " 0.014 2.00e-02 2.50e+03 pdb=" C4 2YR C 7 " 0.261 2.00e-02 2.50e+03 pdb=" C5 2YR C 7 " 0.185 2.00e-02 2.50e+03 pdb=" C6 2YR C 7 " 0.026 2.00e-02 2.50e+03 pdb=" C9 2YR C 7 " -0.719 2.00e-02 2.50e+03 pdb=" N1 2YR C 7 " -0.059 2.00e-02 2.50e+03 pdb=" N3 2YR C 7 " 0.178 2.00e-02 2.50e+03 pdb=" N4 2YR C 7 " 0.423 2.00e-02 2.50e+03 pdb=" O2 2YR C 7 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 699 " 0.095 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO A 700 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 624 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C THR A 624 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 624 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 625 " 0.013 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 8 2.00 - 2.72: 465 2.72 - 3.45: 16203 3.45 - 4.17: 27475 4.17 - 4.90: 48166 Nonbonded interactions: 92317 Sorted by model distance: nonbonded pdb=" CB LYS A 164 " pdb=" CG PRO A 538 " model vdw 1.271 3.840 nonbonded pdb=" CE2 PHE A 165 " pdb=" OD1 ASN A 534 " model vdw 1.637 2.672 nonbonded pdb=" CZ PHE A 165 " pdb=" OD1 ASN A 534 " model vdw 1.694 3.340 nonbonded pdb=" CD ARG A 43 " pdb=" O SER A 161 " model vdw 1.702 3.440 nonbonded pdb=" NE ARG A 43 " pdb=" O SER A 161 " model vdw 1.751 3.120 ... (remaining 92312 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 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 0.228 11569 Z= 0.325 Angle : 0.620 12.649 15886 Z= 0.425 Chirality : 0.043 0.276 1772 Planarity : 0.008 0.300 1836 Dihedral : 18.328 167.752 4537 Min Nonbonded Distance : 1.271 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.83 % Allowed : 2.50 % Favored : 96.67 % 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: -0.88 (0.23), residues: 1226 helix: -0.46 (0.20), residues: 591 sheet: -0.75 (0.45), residues: 134 loop : -0.45 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1121 TYR 0.013 0.001 TYR A 526 PHE 0.015 0.001 PHE A1132 TRP 0.009 0.001 TRP A 958 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.24 (11566) covalent geometry : angle 0.62037 / 0.43 (15886) hydrogen bonds : bond 0.23019 / 24.72 ( 539) hydrogen bonds : angle 7.54779 / 7.67 ( 1507) Misc. bond : bond 0.13485 / 7.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 TYR cc_start: 0.7846 (p90) cc_final: 0.7499 (p90) REVERT: A 34 GLN cc_start: 0.6867 (tp-100) cc_final: 0.6578 (tm-30) REVERT: A 471 LEU cc_start: 0.6945 (mt) cc_final: 0.6729 (mt) REVERT: A 558 VAL cc_start: 0.8422 (p) cc_final: 0.8086 (p) REVERT: A 583 THR cc_start: 0.8415 (p) cc_final: 0.8155 (t) REVERT: A 604 MET cc_start: 0.6809 (mmp) cc_final: 0.5536 (mmt) REVERT: A 720 HIS cc_start: 0.7197 (t-90) cc_final: 0.6885 (t-170) REVERT: A 860 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7739 (tmmt) REVERT: A 937 GLN cc_start: 0.7219 (tp-100) cc_final: 0.6958 (tp-100) REVERT: A 949 LYS cc_start: 0.6963 (tptp) cc_final: 0.6580 (tptp) REVERT: A 1021 ASP cc_start: 0.6997 (m-30) cc_final: 0.6774 (m-30) REVERT: A 1191 ILE cc_start: 0.7994 (mm) cc_final: 0.7787 (mt) REVERT: A 1199 ILE cc_start: 0.8277 (mm) cc_final: 0.7946 (mm) REVERT: A 1215 MET cc_start: 0.7800 (tpt) cc_final: 0.7549 (tpt) REVERT: A 1242 ARG cc_start: 0.6721 (ptp-110) cc_final: 0.6451 (ptp-110) outliers start: 9 outliers final: 2 residues processed: 200 average time/residue: 0.1328 time to fit residues: 36.4006 Evaluate side-chains 179 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 123 optimal weight: 0.0060 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 666 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A1013 GLN A1091 HIS A1229 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151330 restraints weight = 17074.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152075 restraints weight = 8794.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152498 restraints weight = 6292.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152778 restraints weight = 5829.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153109 restraints weight = 5271.148| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11569 Z= 0.149 Angle : 0.613 11.617 15886 Z= 0.326 Chirality : 0.043 0.330 1772 Planarity : 0.005 0.067 1836 Dihedral : 18.861 169.893 2076 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.92 % Allowed : 8.96 % Favored : 90.11 % 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: 0.30 (0.24), residues: 1226 helix: 0.96 (0.21), residues: 610 sheet: -1.02 (0.44), residues: 122 loop : -0.29 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 43 TYR 0.024 0.002 TYR A 687 PHE 0.021 0.001 PHE A 165 TRP 0.010 0.001 TRP A 958 HIS 0.005 0.001 HIS A 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (11566) covalent geometry : angle 0.61327 / 0.33 (15886) hydrogen bonds : bond 0.05525 / 5.91 ( 539) hydrogen bonds : angle 4.90807 / 4.94 ( 1507) Misc. bond : bond 0.00876 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.6928 (tp-100) cc_final: 0.6514 (tm-30) REVERT: A 583 THR cc_start: 0.8446 (p) cc_final: 0.8213 (t) REVERT: A 585 LYS cc_start: 0.8259 (tptt) cc_final: 0.8057 (tptt) REVERT: A 720 HIS cc_start: 0.7046 (t-90) cc_final: 0.6763 (t-170) REVERT: A 841 GLU cc_start: 0.7064 (pm20) cc_final: 0.6624 (pm20) REVERT: A 860 LYS cc_start: 0.8231 (tmmt) cc_final: 0.7780 (tmmt) REVERT: A 911 GLU cc_start: 0.6721 (tp30) cc_final: 0.6342 (tp30) REVERT: A 949 LYS cc_start: 0.6828 (tptp) cc_final: 0.6372 (tptp) REVERT: A 951 ARG cc_start: 0.5879 (ttt90) cc_final: 0.4880 (ttt180) REVERT: A 963 THR cc_start: 0.7923 (p) cc_final: 0.7614 (t) REVERT: A 971 TYR cc_start: 0.7732 (t80) cc_final: 0.7441 (t80) REVERT: A 1021 ASP cc_start: 0.7036 (m-30) cc_final: 0.6766 (m-30) REVERT: A 1099 GLU cc_start: 0.7027 (tp30) cc_final: 0.6807 (tp30) REVERT: A 1191 ILE cc_start: 0.7962 (mm) cc_final: 0.7722 (mt) REVERT: A 1199 ILE cc_start: 0.8271 (mm) cc_final: 0.7932 (mm) REVERT: A 1242 ARG cc_start: 0.6783 (ptp-110) cc_final: 0.6575 (ptp-110) REVERT: A 1260 MET cc_start: 0.7617 (mmt) cc_final: 0.7268 (mmm) outliers start: 10 outliers final: 6 residues processed: 183 average time/residue: 0.1319 time to fit residues: 32.9418 Evaluate side-chains 175 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.189696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146426 restraints weight = 17051.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149768 restraints weight = 8184.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151820 restraints weight = 5265.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152766 restraints weight = 4100.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153509 restraints weight = 3638.774| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11569 Z= 0.159 Angle : 0.564 7.639 15886 Z= 0.301 Chirality : 0.042 0.332 1772 Planarity : 0.004 0.053 1836 Dihedral : 18.779 168.276 2073 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.48 % Allowed : 11.28 % Favored : 87.25 % 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: 0.65 (0.24), residues: 1226 helix: 1.41 (0.21), residues: 611 sheet: -0.85 (0.43), residues: 137 loop : -0.34 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 955 TYR 0.020 0.002 TYR A 595 PHE 0.012 0.001 PHE A 531 TRP 0.011 0.001 TRP A 676 HIS 0.004 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (11566) covalent geometry : angle 0.56418 / 0.30 (15886) hydrogen bonds : bond 0.04360 / 4.69 ( 539) hydrogen bonds : angle 4.47382 / 4.50 ( 1507) Misc. bond : bond 0.00466 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7320 (tp30) cc_final: 0.6960 (tp30) REVERT: A 34 GLN cc_start: 0.7021 (tp-100) cc_final: 0.6528 (tm-30) REVERT: A 43 ARG cc_start: 0.6561 (tpp80) cc_final: 0.6188 (mtt180) REVERT: A 516 LYS cc_start: 0.6605 (tttt) cc_final: 0.6399 (tttt) REVERT: A 583 THR cc_start: 0.8421 (p) cc_final: 0.8203 (t) REVERT: A 585 LYS cc_start: 0.8266 (tptt) cc_final: 0.8024 (tptt) REVERT: A 720 HIS cc_start: 0.7122 (t-90) cc_final: 0.6818 (t70) REVERT: A 776 LYS cc_start: 0.7751 (pptt) cc_final: 0.7440 (pptt) REVERT: A 841 GLU cc_start: 0.7117 (pm20) cc_final: 0.6808 (pm20) REVERT: A 860 LYS cc_start: 0.8181 (tmmt) cc_final: 0.7667 (tmmt) REVERT: A 949 LYS cc_start: 0.6907 (tptp) cc_final: 0.6401 (tptp) REVERT: A 971 TYR cc_start: 0.7674 (t80) cc_final: 0.7294 (t80) REVERT: A 1021 ASP cc_start: 0.7090 (m-30) cc_final: 0.6790 (m-30) REVERT: A 1099 GLU cc_start: 0.7109 (tp30) cc_final: 0.6840 (tp30) REVERT: A 1191 ILE cc_start: 0.7945 (mm) cc_final: 0.7744 (mt) REVERT: A 1199 ILE cc_start: 0.8231 (mm) cc_final: 0.7952 (mm) REVERT: A 1242 ARG cc_start: 0.6855 (ptp-110) cc_final: 0.6574 (ptp-110) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 0.1335 time to fit residues: 31.4295 Evaluate side-chains 178 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 HIS A1105 HIS ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.188805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144702 restraints weight = 17167.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148054 restraints weight = 8376.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149924 restraints weight = 5448.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151331 restraints weight = 4292.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151872 restraints weight = 3758.223| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11569 Z= 0.168 Angle : 0.564 10.721 15886 Z= 0.299 Chirality : 0.043 0.329 1772 Planarity : 0.004 0.047 1836 Dihedral : 18.803 167.972 2073 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 12.57 % Favored : 85.49 % 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: 0.83 (0.25), residues: 1226 helix: 1.63 (0.22), residues: 612 sheet: -0.90 (0.42), residues: 135 loop : -0.34 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 947 TYR 0.021 0.002 TYR A 595 PHE 0.026 0.001 PHE A1103 TRP 0.009 0.001 TRP A 676 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (11566) covalent geometry : angle 0.56380 / 0.30 (15886) hydrogen bonds : bond 0.03857 / 4.20 ( 539) hydrogen bonds : angle 4.28173 / 4.27 ( 1507) Misc. bond : bond 0.00091 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7090 (tp-100) cc_final: 0.6570 (tm-30) REVERT: A 44 ASN cc_start: 0.7627 (t0) cc_final: 0.7352 (t0) REVERT: A 568 MET cc_start: 0.7875 (mpp) cc_final: 0.7269 (mtp) REVERT: A 585 LYS cc_start: 0.8267 (tptt) cc_final: 0.8000 (tptt) REVERT: A 604 MET cc_start: 0.6998 (mmp) cc_final: 0.6225 (mmt) REVERT: A 720 HIS cc_start: 0.7216 (t-90) cc_final: 0.6897 (t70) REVERT: A 841 GLU cc_start: 0.7136 (pm20) cc_final: 0.6844 (pm20) REVERT: A 860 LYS cc_start: 0.8210 (tmmt) cc_final: 0.7799 (tmmt) REVERT: A 861 ASP cc_start: 0.7382 (m-30) cc_final: 0.7075 (m-30) REVERT: A 949 LYS cc_start: 0.6906 (tptp) cc_final: 0.6382 (tptp) REVERT: A 963 THR cc_start: 0.7921 (p) cc_final: 0.7522 (t) REVERT: A 971 TYR cc_start: 0.7643 (t80) cc_final: 0.7243 (t80) REVERT: A 1021 ASP cc_start: 0.7073 (m-30) cc_final: 0.6759 (m-30) REVERT: A 1099 GLU cc_start: 0.7123 (tp30) cc_final: 0.6774 (tp30) REVERT: A 1199 ILE cc_start: 0.8207 (mm) cc_final: 0.7930 (mm) REVERT: A 1215 MET cc_start: 0.8024 (tpp) cc_final: 0.7729 (tpp) REVERT: A 1242 ARG cc_start: 0.6860 (ptp-110) cc_final: 0.6604 (ptp-110) outliers start: 21 outliers final: 15 residues processed: 176 average time/residue: 0.1337 time to fit residues: 31.6969 Evaluate side-chains 177 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 647 ASN A 878 ASN A1044 GLN A1091 HIS ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.188221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147244 restraints weight = 17074.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148011 restraints weight = 9278.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149503 restraints weight = 6528.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149622 restraints weight = 5415.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150000 restraints weight = 4994.525| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11569 Z= 0.154 Angle : 0.555 8.286 15886 Z= 0.294 Chirality : 0.042 0.327 1772 Planarity : 0.004 0.085 1836 Dihedral : 18.816 169.057 2073 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 13.68 % Favored : 84.10 % 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: 0.95 (0.25), residues: 1226 helix: 1.74 (0.22), residues: 614 sheet: -0.92 (0.42), residues: 135 loop : -0.30 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 699 TYR 0.020 0.001 TYR A 595 PHE 0.010 0.001 PHE A 531 TRP 0.008 0.001 TRP A1085 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11566) covalent geometry : angle 0.55518 / 0.29 (15886) hydrogen bonds : bond 0.03655 / 3.97 ( 539) hydrogen bonds : angle 4.13023 / 4.08 ( 1507) Misc. bond : bond 0.00071 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6554 (tm-30) REVERT: A 44 ASN cc_start: 0.7614 (t0) cc_final: 0.7299 (t0) REVERT: A 568 MET cc_start: 0.7793 (mpp) cc_final: 0.7182 (mtp) REVERT: A 720 HIS cc_start: 0.7134 (t-90) cc_final: 0.6838 (t70) REVERT: A 798 MET cc_start: 0.6251 (tmm) cc_final: 0.5985 (tmm) REVERT: A 841 GLU cc_start: 0.7281 (pm20) cc_final: 0.7041 (pm20) REVERT: A 860 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7752 (tmmt) REVERT: A 861 ASP cc_start: 0.7410 (m-30) cc_final: 0.7148 (m-30) REVERT: A 949 LYS cc_start: 0.7120 (tptp) cc_final: 0.6597 (tptp) REVERT: A 971 TYR cc_start: 0.7610 (t80) cc_final: 0.7128 (t80) REVERT: A 1021 ASP cc_start: 0.6961 (m-30) cc_final: 0.6697 (m-30) REVERT: A 1099 GLU cc_start: 0.7079 (tp30) cc_final: 0.6717 (tp30) REVERT: A 1199 ILE cc_start: 0.8141 (mm) cc_final: 0.7941 (mm) REVERT: A 1215 MET cc_start: 0.8029 (tpp) cc_final: 0.7750 (tpp) REVERT: A 1242 ARG cc_start: 0.6885 (ptp-110) cc_final: 0.6659 (ptp-110) outliers start: 24 outliers final: 18 residues processed: 175 average time/residue: 0.1375 time to fit residues: 32.2967 Evaluate side-chains 177 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 111 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 0.0030 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.189219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149173 restraints weight = 17329.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149519 restraints weight = 9529.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150291 restraints weight = 6610.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150502 restraints weight = 5854.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150634 restraints weight = 5331.170| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11569 Z= 0.115 Angle : 0.531 7.610 15886 Z= 0.281 Chirality : 0.041 0.323 1772 Planarity : 0.004 0.045 1836 Dihedral : 18.807 169.970 2073 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 14.79 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1226 helix: 1.89 (0.22), residues: 614 sheet: -0.87 (0.42), residues: 133 loop : -0.30 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 947 TYR 0.018 0.001 TYR A 595 PHE 0.011 0.001 PHE A 598 TRP 0.008 0.001 TRP A 676 HIS 0.010 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (11566) covalent geometry : angle 0.53095 / 0.28 (15886) hydrogen bonds : bond 0.03368 / 3.64 ( 539) hydrogen bonds : angle 4.03055 / 4.00 ( 1507) Misc. bond : bond 0.00034 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7023 (tp-100) cc_final: 0.6519 (tm-30) REVERT: A 44 ASN cc_start: 0.7561 (t0) cc_final: 0.7250 (t0) REVERT: A 568 MET cc_start: 0.7785 (mpp) cc_final: 0.7146 (mtp) REVERT: A 720 HIS cc_start: 0.7114 (t-90) cc_final: 0.6832 (t70) REVERT: A 798 MET cc_start: 0.6285 (tmm) cc_final: 0.6029 (tmm) REVERT: A 841 GLU cc_start: 0.7265 (pm20) cc_final: 0.6997 (pm20) REVERT: A 860 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7818 (tmmt) REVERT: A 861 ASP cc_start: 0.7401 (m-30) cc_final: 0.7147 (m-30) REVERT: A 949 LYS cc_start: 0.7115 (tptp) cc_final: 0.6544 (tptp) REVERT: A 971 TYR cc_start: 0.7564 (t80) cc_final: 0.7070 (t80) REVERT: A 1021 ASP cc_start: 0.6927 (m-30) cc_final: 0.6684 (m-30) REVERT: A 1099 GLU cc_start: 0.7096 (tp30) cc_final: 0.6709 (tp30) REVERT: A 1188 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7064 (tm-30) REVERT: A 1199 ILE cc_start: 0.8102 (mm) cc_final: 0.7892 (mm) REVERT: A 1215 MET cc_start: 0.8005 (tpp) cc_final: 0.7742 (tpp) REVERT: A 1242 ARG cc_start: 0.6883 (ptp-110) cc_final: 0.6639 (ptp-110) outliers start: 21 outliers final: 18 residues processed: 177 average time/residue: 0.1305 time to fit residues: 31.4075 Evaluate side-chains 183 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.188586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.148206 restraints weight = 16862.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148806 restraints weight = 9160.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149744 restraints weight = 6504.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149994 restraints weight = 5559.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150574 restraints weight = 5094.363| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11569 Z= 0.154 Angle : 0.553 8.748 15886 Z= 0.290 Chirality : 0.042 0.328 1772 Planarity : 0.004 0.050 1836 Dihedral : 18.839 169.737 2073 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.03 % Allowed : 15.06 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1226 helix: 1.95 (0.22), residues: 619 sheet: -0.89 (0.41), residues: 135 loop : -0.34 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.024 0.001 TYR A 879 PHE 0.014 0.001 PHE A1154 TRP 0.013 0.001 TRP A 676 HIS 0.009 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11566) covalent geometry : angle 0.55268 / 0.29 (15886) hydrogen bonds : bond 0.03408 / 3.72 ( 539) hydrogen bonds : angle 3.95559 / 3.89 ( 1507) Misc. bond : bond 0.00033 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7087 (tp-100) cc_final: 0.6527 (tm-30) REVERT: A 43 ARG cc_start: 0.6778 (tpp80) cc_final: 0.6269 (mtp180) REVERT: A 44 ASN cc_start: 0.7594 (t0) cc_final: 0.7243 (t0) REVERT: A 568 MET cc_start: 0.7827 (mpp) cc_final: 0.7269 (mtp) REVERT: A 720 HIS cc_start: 0.7146 (t-90) cc_final: 0.6825 (t70) REVERT: A 798 MET cc_start: 0.6313 (tmm) cc_final: 0.6052 (tmm) REVERT: A 841 GLU cc_start: 0.7256 (pm20) cc_final: 0.7007 (pm20) REVERT: A 860 LYS cc_start: 0.8231 (tmmt) cc_final: 0.7729 (tmmt) REVERT: A 861 ASP cc_start: 0.7484 (m-30) cc_final: 0.7171 (m-30) REVERT: A 949 LYS cc_start: 0.7033 (tptp) cc_final: 0.6505 (tptp) REVERT: A 971 TYR cc_start: 0.7561 (t80) cc_final: 0.7015 (t80) REVERT: A 1021 ASP cc_start: 0.6988 (m-30) cc_final: 0.6705 (m-30) REVERT: A 1099 GLU cc_start: 0.7117 (tp30) cc_final: 0.6651 (tp30) REVERT: A 1199 ILE cc_start: 0.8134 (mm) cc_final: 0.7895 (mm) REVERT: A 1215 MET cc_start: 0.8029 (tpp) cc_final: 0.7773 (tpp) REVERT: A 1242 ARG cc_start: 0.6908 (ptp-110) cc_final: 0.6695 (ptp-110) outliers start: 22 outliers final: 20 residues processed: 181 average time/residue: 0.1268 time to fit residues: 31.1875 Evaluate side-chains 184 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 95 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.187983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147524 restraints weight = 16948.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148567 restraints weight = 9290.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149436 restraints weight = 6362.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149630 restraints weight = 5869.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150143 restraints weight = 5137.957| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11569 Z= 0.156 Angle : 0.552 7.496 15886 Z= 0.292 Chirality : 0.042 0.329 1772 Planarity : 0.004 0.051 1836 Dihedral : 18.796 170.110 2073 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.94 % Allowed : 15.90 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1226 helix: 1.91 (0.22), residues: 623 sheet: -0.92 (0.41), residues: 135 loop : -0.30 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1226 TYR 0.026 0.001 TYR A 879 PHE 0.022 0.001 PHE A 513 TRP 0.008 0.001 TRP A1085 HIS 0.009 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (11566) covalent geometry : angle 0.55196 / 0.29 (15886) hydrogen bonds : bond 0.03398 / 3.71 ( 539) hydrogen bonds : angle 3.95529 / 3.92 ( 1507) Misc. bond : bond 0.00042 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7128 (tp-100) cc_final: 0.6924 (tm-30) REVERT: A 43 ARG cc_start: 0.6669 (tpp80) cc_final: 0.6101 (mtp180) REVERT: A 44 ASN cc_start: 0.7596 (t0) cc_final: 0.7244 (t0) REVERT: A 513 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 516 LYS cc_start: 0.6599 (tttt) cc_final: 0.6223 (tttp) REVERT: A 568 MET cc_start: 0.7824 (mpp) cc_final: 0.7312 (mtp) REVERT: A 720 HIS cc_start: 0.7148 (t-90) cc_final: 0.6945 (t70) REVERT: A 798 MET cc_start: 0.6335 (tmm) cc_final: 0.6075 (tmm) REVERT: A 841 GLU cc_start: 0.7257 (pm20) cc_final: 0.7034 (mp0) REVERT: A 860 LYS cc_start: 0.8220 (tmmt) cc_final: 0.7692 (tmmt) REVERT: A 861 ASP cc_start: 0.7519 (m-30) cc_final: 0.7191 (m-30) REVERT: A 949 LYS cc_start: 0.6941 (tptp) cc_final: 0.6445 (tptp) REVERT: A 971 TYR cc_start: 0.7547 (t80) cc_final: 0.7016 (t80) REVERT: A 1021 ASP cc_start: 0.6986 (m-30) cc_final: 0.6703 (m-30) REVERT: A 1099 GLU cc_start: 0.7124 (tp30) cc_final: 0.6623 (tp30) REVERT: A 1199 ILE cc_start: 0.8115 (mm) cc_final: 0.7897 (mm) REVERT: A 1215 MET cc_start: 0.8023 (tpp) cc_final: 0.7765 (tpp) REVERT: A 1242 ARG cc_start: 0.6933 (ptp-110) cc_final: 0.6732 (ptp-110) outliers start: 21 outliers final: 19 residues processed: 177 average time/residue: 0.1219 time to fit residues: 29.3831 Evaluate side-chains 184 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 87 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.188371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147921 restraints weight = 16868.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149435 restraints weight = 8441.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150211 restraints weight = 5936.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150308 restraints weight = 5150.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150511 restraints weight = 4913.360| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11569 Z= 0.138 Angle : 0.540 7.187 15886 Z= 0.285 Chirality : 0.041 0.326 1772 Planarity : 0.004 0.053 1836 Dihedral : 18.734 170.845 2073 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.22 % Allowed : 15.80 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1226 helix: 1.98 (0.22), residues: 623 sheet: -0.92 (0.42), residues: 135 loop : -0.30 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 725 TYR 0.027 0.001 TYR A 879 PHE 0.012 0.001 PHE A 513 TRP 0.009 0.001 TRP A 676 HIS 0.009 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (11566) covalent geometry : angle 0.53998 / 0.29 (15886) hydrogen bonds : bond 0.03272 / 3.55 ( 539) hydrogen bonds : angle 3.90236 / 3.87 ( 1507) Misc. bond : bond 0.00027 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7302 (tp30) cc_final: 0.6967 (tp30) REVERT: A 44 ASN cc_start: 0.7594 (t0) cc_final: 0.7310 (t0) REVERT: A 513 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.7044 (t80) REVERT: A 568 MET cc_start: 0.7828 (mpp) cc_final: 0.7316 (mtp) REVERT: A 720 HIS cc_start: 0.7152 (t-90) cc_final: 0.6822 (t70) REVERT: A 798 MET cc_start: 0.6357 (tmm) cc_final: 0.6083 (tmm) REVERT: A 841 GLU cc_start: 0.7252 (pm20) cc_final: 0.7039 (mp0) REVERT: A 860 LYS cc_start: 0.8204 (tmmt) cc_final: 0.7699 (tmmt) REVERT: A 861 ASP cc_start: 0.7581 (m-30) cc_final: 0.7268 (m-30) REVERT: A 921 ASP cc_start: 0.7146 (p0) cc_final: 0.6933 (p0) REVERT: A 933 ASN cc_start: 0.7608 (p0) cc_final: 0.7382 (p0) REVERT: A 949 LYS cc_start: 0.6920 (tptp) cc_final: 0.6441 (tptp) REVERT: A 966 ASP cc_start: 0.6539 (m-30) cc_final: 0.6217 (m-30) REVERT: A 971 TYR cc_start: 0.7530 (t80) cc_final: 0.6999 (t80) REVERT: A 1021 ASP cc_start: 0.6963 (m-30) cc_final: 0.6684 (m-30) REVERT: A 1099 GLU cc_start: 0.7116 (tp30) cc_final: 0.6622 (tp30) REVERT: A 1199 ILE cc_start: 0.8101 (mm) cc_final: 0.7880 (mm) REVERT: A 1215 MET cc_start: 0.8027 (tpp) cc_final: 0.7814 (tpp) outliers start: 24 outliers final: 21 residues processed: 178 average time/residue: 0.1129 time to fit residues: 27.4218 Evaluate side-chains 184 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 120 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 666 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148976 restraints weight = 16949.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152278 restraints weight = 8479.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154076 restraints weight = 5513.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155413 restraints weight = 4357.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156060 restraints weight = 3801.851| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11569 Z= 0.139 Angle : 0.545 7.227 15886 Z= 0.287 Chirality : 0.041 0.327 1772 Planarity : 0.004 0.052 1836 Dihedral : 18.710 171.351 2073 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 15.99 % Favored : 81.89 % 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: 1.20 (0.25), residues: 1226 helix: 2.02 (0.21), residues: 622 sheet: -0.91 (0.42), residues: 135 loop : -0.30 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 725 TYR 0.028 0.001 TYR A 879 PHE 0.013 0.001 PHE A1154 TRP 0.008 0.001 TRP A1085 HIS 0.009 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11566) covalent geometry : angle 0.54535 / 0.29 (15886) hydrogen bonds : bond 0.03222 / 3.51 ( 539) hydrogen bonds : angle 3.87259 / 3.85 ( 1507) Misc. bond : bond 0.00041 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7338 (tp30) cc_final: 0.7003 (tp30) REVERT: A 43 ARG cc_start: 0.6753 (tpp80) cc_final: 0.6045 (mtt180) REVERT: A 44 ASN cc_start: 0.7637 (t0) cc_final: 0.7289 (t0) REVERT: A 513 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.7077 (t80) REVERT: A 568 MET cc_start: 0.7911 (mpp) cc_final: 0.7443 (mtp) REVERT: A 720 HIS cc_start: 0.7176 (t-90) cc_final: 0.6818 (t70) REVERT: A 798 MET cc_start: 0.6279 (tmm) cc_final: 0.6023 (tmm) REVERT: A 860 LYS cc_start: 0.8177 (tmmt) cc_final: 0.7650 (tmmt) REVERT: A 861 ASP cc_start: 0.7556 (m-30) cc_final: 0.7236 (m-30) REVERT: A 949 LYS cc_start: 0.6890 (tptp) cc_final: 0.6393 (tptp) REVERT: A 966 ASP cc_start: 0.6582 (m-30) cc_final: 0.6249 (m-30) REVERT: A 971 TYR cc_start: 0.7501 (t80) cc_final: 0.6981 (t80) REVERT: A 1021 ASP cc_start: 0.7004 (m-30) cc_final: 0.6719 (m-30) REVERT: A 1099 GLU cc_start: 0.7111 (tp30) cc_final: 0.6566 (tp30) REVERT: A 1199 ILE cc_start: 0.8085 (mm) cc_final: 0.7877 (mm) REVERT: A 1215 MET cc_start: 0.8039 (tpp) cc_final: 0.7816 (tpp) outliers start: 23 outliers final: 22 residues processed: 180 average time/residue: 0.1260 time to fit residues: 31.0922 Evaluate side-chains 187 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 937 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS ** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.190867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148194 restraints weight = 16883.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151542 restraints weight = 8251.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153508 restraints weight = 5271.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154868 restraints weight = 4106.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155255 restraints weight = 3564.049| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11569 Z= 0.167 Angle : 0.568 12.727 15886 Z= 0.295 Chirality : 0.042 0.330 1772 Planarity : 0.004 0.054 1836 Dihedral : 18.729 170.694 2073 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.03 % Allowed : 16.08 % Favored : 81.89 % 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: 1.17 (0.25), residues: 1226 helix: 2.02 (0.21), residues: 623 sheet: -0.90 (0.42), residues: 135 loop : -0.34 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.023 0.001 TYR A 879 PHE 0.016 0.001 PHE A1052 TRP 0.009 0.001 TRP A1085 HIS 0.012 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (11566) covalent geometry : angle 0.56777 / 0.29 (15886) hydrogen bonds : bond 0.03324 / 3.63 ( 539) hydrogen bonds : angle 3.88907 / 3.88 ( 1507) Misc. bond : bond 0.00047 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.76 seconds wall clock time: 34 minutes 9.35 seconds (2049.35 seconds total)