Starting phenix.real_space_refine on Wed Mar 4 06:48:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrb_21366/03_2026/6vrb_21366.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 37 5.16 5 C 7210 2.51 5 N 1948 2.21 5 O 2335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11581 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1093 Classifications: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 30} Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8574 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 23, 'TRANS': 1007} Chain breaks: 2 Chain: "C" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1914 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11581 At special positions: 0 Unit cell: (119.88, 93.96, 106.92, 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 37 16.00 P 51 15.00 O 2335 8.00 N 1948 7.00 C 7210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 511.7 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 59.5% alpha, 2.2% beta 5 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.604A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.705A pdb=" N VAL A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.688A pdb=" N VAL A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.901A pdb=" N PHE A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.711A pdb=" N ASP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 203 removed outlier: 3.719A pdb=" N TRP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.569A pdb=" N ILE A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.659A pdb=" N GLU A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 262 through 278 removed outlier: 3.550A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.563A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.667A pdb=" N ASN A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 355 through 388 removed outlier: 3.693A pdb=" N ILE A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.790A pdb=" N LYS A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.784A pdb=" N ILE A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.587A pdb=" N ARG A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Proline residue: A 443 - end of helix removed outlier: 3.827A pdb=" N GLU A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.646A pdb=" N ILE A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.564A pdb=" N LEU A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 526 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 528 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.589A pdb=" N SER A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.907A pdb=" N GLN A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.593A pdb=" N PHE A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.673A pdb=" N TYR A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.814A pdb=" N LYS A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 690 removed outlier: 3.726A pdb=" N LYS A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.588A pdb=" N MET A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 748 removed outlier: 3.517A pdb=" N LYS A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 771 removed outlier: 3.825A pdb=" N GLU A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.845A pdb=" N GLU A 782 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.549A pdb=" N TRP A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 804 removed outlier: 4.115A pdb=" N LEU A 803 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 804 " --> pdb=" O GLU A 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 800 through 804' Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.789A pdb=" N TYR A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 removed outlier: 3.523A pdb=" N GLU A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.996A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 876 removed outlier: 3.710A pdb=" N ILE A 874 " --> pdb=" O HIS A 870 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 882 through 907 Processing helix chain 'A' and resid 909 through 946 removed outlier: 3.618A pdb=" N ARG A 924 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 931 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 946 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.639A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.651A pdb=" N LYS A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A1020 " --> pdb=" O ARG A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1044 removed outlier: 3.609A pdb=" N ARG A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.719A pdb=" N ALA A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.740A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.718A pdb=" N CYS A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 removed outlier: 3.571A pdb=" N PHE C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 54 removed outlier: 4.029A pdb=" N LYS C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 54 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.536A pdb=" N CYS C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.826A pdb=" N LYS C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 176 removed outlier: 3.556A pdb=" N THR C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 200 removed outlier: 3.605A pdb=" N SER C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.415A pdb=" N ILE C 204 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 229 removed outlier: 3.654A pdb=" N GLN C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA4, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 126 removed outlier: 3.800A pdb=" N THR C 125 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 141 " --> pdb=" O THR C 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 432 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1871 1.32 - 1.44: 3397 1.44 - 1.56: 6486 1.56 - 1.69: 102 1.69 - 1.81: 61 Bond restraints: 11917 Sorted by residual: bond pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" N ILE A 170 " pdb=" CA ILE A 170 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.51e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14894 2.09 - 4.19: 1210 4.19 - 6.28: 119 6.28 - 8.37: 35 8.37 - 10.47: 14 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N GLU A 431 " pdb=" CA GLU A 431 " pdb=" C GLU A 431 " ideal model delta sigma weight residual 114.62 105.17 9.45 1.14e+00 7.69e-01 6.87e+01 angle pdb=" N VAL A 595 " pdb=" CA VAL A 595 " pdb=" C VAL A 595 " ideal model delta sigma weight residual 110.72 104.95 5.77 1.01e+00 9.80e-01 3.27e+01 angle pdb=" N LYS C 65 " pdb=" CA LYS C 65 " pdb=" C LYS C 65 " ideal model delta sigma weight residual 111.02 117.58 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ARG A 316 " pdb=" N ASN A 317 " pdb=" CA ASN A 317 " ideal model delta sigma weight residual 120.28 127.07 -6.79 1.34e+00 5.57e-01 2.57e+01 angle pdb=" C THR A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta sigma weight residual 121.19 128.99 -7.80 1.59e+00 3.96e-01 2.41e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7102 35.54 - 71.09: 206 71.09 - 106.63: 20 106.63 - 142.17: 0 142.17 - 177.71: 4 Dihedral angle restraints: 7332 sinusoidal: 3557 harmonic: 3775 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 232.00 54.29 177.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 37 " pdb=" C1' U B 37 " pdb=" N1 U B 37 " pdb=" C2 U B 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.39 -177.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 51 " pdb=" C1' U B 51 " pdb=" N1 U B 51 " pdb=" C2 U B 51 " ideal model delta sinusoidal sigma weight residual 232.00 58.11 173.89 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1486 0.095 - 0.191: 289 0.191 - 0.286: 43 0.286 - 0.381: 1 0.381 - 0.477: 1 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA LYS C 11 " pdb=" N LYS C 11 " pdb=" C LYS C 11 " pdb=" CB LYS C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN A 532 " pdb=" N ASN A 532 " pdb=" C ASN A 532 " pdb=" CB ASN A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL A 527 " pdb=" CA VAL A 527 " pdb=" CG1 VAL A 527 " pdb=" CG2 VAL A 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1817 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 5 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE C 5 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE C 5 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 508 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN A 508 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN A 508 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 509 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C MET A 594 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 595 " 0.018 2.00e-02 2.50e+03 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 60 2.48 - 3.09: 7248 3.09 - 3.69: 17273 3.69 - 4.30: 26170 4.30 - 4.90: 41661 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG A 212 " pdb=" OG SER A 213 " model vdw 1.877 3.040 nonbonded pdb=" OH TYR C 197 " pdb=" OH TYR C 213 " model vdw 2.166 3.040 nonbonded pdb=" O TYR C 197 " pdb=" O SER C 200 " model vdw 2.178 3.040 nonbonded pdb=" O6 G B 1 " pdb=" O ASN A 309 " model vdw 2.216 3.040 nonbonded pdb=" O2' G B 15 " pdb=" NH1 ARG A 129 " model vdw 2.231 3.120 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.600 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.009 0.089 11917 Z= 0.538 Angle : 1.205 10.467 16272 Z= 0.768 Chirality : 0.076 0.477 1820 Planarity : 0.006 0.067 1873 Dihedral : 16.053 177.714 4872 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.12 % Allowed : 8.95 % Favored : 87.92 % Cbeta Deviations : 0.16 % 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: -4.13 (0.21), residues: 1252 helix: -2.70 (0.17), residues: 725 sheet: -3.03 (0.56), residues: 75 loop : -2.40 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 763 TYR 0.030 0.003 TYR A1046 PHE 0.042 0.003 PHE C 63 TRP 0.037 0.004 TRP C 64 HIS 0.013 0.002 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00907 (11917) covalent geometry : angle 1.20495 (16272) hydrogen bonds : bond 0.32656 ( 445) hydrogen bonds : angle 9.54248 ( 1274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.455 Fit side-chains REVERT: A 743 MET cc_start: 0.8997 (ttm) cc_final: 0.8778 (ttm) REVERT: C 170 ILE cc_start: 0.8619 (tt) cc_final: 0.8402 (mp) outliers start: 37 outliers final: 3 residues processed: 298 average time/residue: 0.6235 time to fit residues: 199.2383 Evaluate side-chains 133 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain C residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 ASN A 127 ASN A 153 ASN A 165 GLN A 285 ASN A 289 ASN A 329 HIS A 333 ASN A 410 HIS A 532 ASN A 576 ASN A 598 GLN A 654 GLN A 714 HIS A 751 GLN A 772 ASN A 866 GLN A 915 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1111 GLN C 129 HIS C 180 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147277 restraints weight = 13653.473| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.68 r_work: 0.3129 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11917 Z= 0.152 Angle : 0.665 9.872 16272 Z= 0.360 Chirality : 0.041 0.192 1820 Planarity : 0.005 0.061 1873 Dihedral : 16.239 178.355 2125 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.98 % Allowed : 16.81 % Favored : 78.21 % 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: -2.57 (0.22), residues: 1252 helix: -1.26 (0.18), residues: 734 sheet: -2.56 (0.64), residues: 72 loop : -2.07 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1016 TYR 0.026 0.002 TYR A1046 PHE 0.015 0.002 PHE A 130 TRP 0.017 0.002 TRP C 50 HIS 0.005 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00322 (11917) covalent geometry : angle 0.66500 (16272) hydrogen bonds : bond 0.06499 ( 445) hydrogen bonds : angle 4.77404 ( 1274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 225 LEU cc_start: 0.7492 (mp) cc_final: 0.6995 (tt) REVERT: A 235 SER cc_start: 0.7373 (t) cc_final: 0.6988 (m) REVERT: A 330 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8223 (ptp-170) REVERT: A 383 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7294 (tp) REVERT: A 445 ARG cc_start: 0.4168 (OUTLIER) cc_final: 0.3838 (tpm170) REVERT: A 667 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8539 (mtpt) REVERT: A 818 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (mt) REVERT: A 867 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: A 935 ASP cc_start: 0.8252 (m-30) cc_final: 0.7974 (m-30) REVERT: A 1017 ASN cc_start: 0.7653 (t0) cc_final: 0.7407 (m-40) REVERT: A 1087 GLN cc_start: 0.8300 (mt0) cc_final: 0.8076 (mt0) REVERT: C 17 ASN cc_start: 0.8385 (m-40) cc_final: 0.8158 (m110) REVERT: C 19 MET cc_start: 0.8498 (mmt) cc_final: 0.8195 (mmt) REVERT: C 170 ILE cc_start: 0.8452 (tt) cc_final: 0.8048 (mt) REVERT: C 189 ILE cc_start: 0.7638 (mm) cc_final: 0.7437 (mm) outliers start: 59 outliers final: 14 residues processed: 223 average time/residue: 0.6404 time to fit residues: 153.3120 Evaluate side-chains 155 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 867 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 165 GLN A 333 ASN A 357 ASN A 410 HIS A 462 ASN A 659 GLN A 714 HIS A 751 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.160182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129569 restraints weight = 13433.248| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.76 r_work: 0.2859 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11917 Z= 0.147 Angle : 0.612 10.097 16272 Z= 0.330 Chirality : 0.042 0.192 1820 Planarity : 0.004 0.059 1873 Dihedral : 16.024 178.150 2123 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.08 % Allowed : 18.07 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1252 helix: -0.39 (0.19), residues: 741 sheet: -2.42 (0.64), residues: 72 loop : -1.89 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 202 TYR 0.023 0.001 TYR A1046 PHE 0.012 0.002 PHE A 130 TRP 0.022 0.002 TRP C 137 HIS 0.006 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00319 (11917) covalent geometry : angle 0.61225 (16272) hydrogen bonds : bond 0.06075 ( 445) hydrogen bonds : angle 4.03576 ( 1274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.524 Fit side-chains REVERT: A 41 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: A 65 GLN cc_start: 0.8328 (mt0) cc_final: 0.8008 (mm-40) REVERT: A 132 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7504 (ptpt) REVERT: A 149 ARG cc_start: 0.7718 (ptm160) cc_final: 0.7445 (ptm160) REVERT: A 156 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7807 (tp40) REVERT: A 237 SER cc_start: 0.9169 (t) cc_final: 0.8948 (m) REVERT: A 246 THR cc_start: 0.8614 (p) cc_final: 0.8283 (p) REVERT: A 280 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: A 316 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7439 (ttp80) REVERT: A 351 GLU cc_start: 0.7914 (pm20) cc_final: 0.7518 (tm-30) REVERT: A 383 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 487 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8070 (mtpp) REVERT: A 586 GLN cc_start: 0.8772 (mt0) cc_final: 0.8414 (mm110) REVERT: A 667 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: A 710 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8401 (mm-30) REVERT: A 738 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9064 (mt-10) REVERT: A 784 PHE cc_start: 0.8116 (m-80) cc_final: 0.7772 (m-80) REVERT: A 858 ASP cc_start: 0.8342 (t0) cc_final: 0.8123 (t0) REVERT: A 1007 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4590 (tp) REVERT: A 1016 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7615 (ptp-170) REVERT: A 1017 ASN cc_start: 0.7688 (t0) cc_final: 0.7475 (m-40) REVERT: A 1087 GLN cc_start: 0.8815 (mt0) cc_final: 0.8574 (mt0) REVERT: C 19 MET cc_start: 0.8740 (mmt) cc_final: 0.8446 (mmt) REVERT: C 25 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: C 208 TYR cc_start: 0.7185 (t80) cc_final: 0.6730 (t80) outliers start: 72 outliers final: 19 residues processed: 228 average time/residue: 0.6517 time to fit residues: 159.6546 Evaluate side-chains 150 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 462 ASN A 751 GLN A 793 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121189 restraints weight = 13398.539| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.68 r_work: 0.2746 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11917 Z= 0.179 Angle : 0.639 11.207 16272 Z= 0.342 Chirality : 0.043 0.187 1820 Planarity : 0.004 0.058 1873 Dihedral : 15.980 179.482 2121 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.42 % Allowed : 18.67 % Favored : 74.92 % 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: -1.23 (0.23), residues: 1252 helix: 0.04 (0.19), residues: 745 sheet: -2.43 (0.62), residues: 73 loop : -1.92 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 202 TYR 0.023 0.002 TYR C 162 PHE 0.014 0.002 PHE A 130 TRP 0.027 0.002 TRP C 137 HIS 0.005 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00405 (11917) covalent geometry : angle 0.63851 (16272) hydrogen bonds : bond 0.06659 ( 445) hydrogen bonds : angle 4.01030 ( 1274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 145 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: A 65 GLN cc_start: 0.8493 (mt0) cc_final: 0.8152 (mm-40) REVERT: A 116 ASP cc_start: 0.7709 (m-30) cc_final: 0.7473 (m-30) REVERT: A 132 LYS cc_start: 0.7980 (mmtp) cc_final: 0.7571 (ptpt) REVERT: A 149 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7505 (ptm160) REVERT: A 177 LYS cc_start: 0.8774 (tptp) cc_final: 0.8496 (tppt) REVERT: A 246 THR cc_start: 0.9094 (p) cc_final: 0.8734 (p) REVERT: A 383 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 483 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: A 487 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8234 (mtpp) REVERT: A 513 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8865 (t) REVERT: A 591 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9156 (tt) REVERT: A 633 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: A 710 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8487 (mm-30) REVERT: A 735 GLN cc_start: 0.8792 (mp10) cc_final: 0.8482 (mp10) REVERT: A 784 PHE cc_start: 0.8542 (m-80) cc_final: 0.8087 (m-80) REVERT: A 888 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (tttp) REVERT: A 1007 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4474 (tp) REVERT: A 1017 ASN cc_start: 0.7858 (t0) cc_final: 0.7620 (m-40) REVERT: A 1087 GLN cc_start: 0.9036 (mt0) cc_final: 0.8763 (mt0) REVERT: C 19 MET cc_start: 0.8837 (mmt) cc_final: 0.8617 (mmt) REVERT: C 25 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8465 (mm-30) REVERT: C 174 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7363 (ttmm) REVERT: C 215 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6697 (pp20) outliers start: 76 outliers final: 21 residues processed: 200 average time/residue: 0.6591 time to fit residues: 141.1151 Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 888 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 7.9990 chunk 118 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 360 GLN A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125565 restraints weight = 13395.454| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.46 r_work: 0.2827 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11917 Z= 0.124 Angle : 0.551 10.250 16272 Z= 0.298 Chirality : 0.040 0.189 1820 Planarity : 0.003 0.056 1873 Dihedral : 15.892 177.781 2121 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.48 % Allowed : 20.86 % Favored : 74.66 % 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: -0.74 (0.24), residues: 1252 helix: 0.50 (0.20), residues: 744 sheet: -2.13 (0.66), residues: 73 loop : -1.88 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.016 0.001 TYR A1046 PHE 0.010 0.001 PHE C 91 TRP 0.029 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00265 (11917) covalent geometry : angle 0.55137 (16272) hydrogen bonds : bond 0.05366 ( 445) hydrogen bonds : angle 3.79089 ( 1274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: A 65 GLN cc_start: 0.8416 (mt0) cc_final: 0.8144 (mm-40) REVERT: A 149 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7569 (ptm160) REVERT: A 177 LYS cc_start: 0.8768 (tptp) cc_final: 0.8510 (mtpt) REVERT: A 246 THR cc_start: 0.9060 (p) cc_final: 0.8712 (p) REVERT: A 383 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7825 (tp) REVERT: A 487 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8191 (mtpp) REVERT: A 505 LEU cc_start: 0.9315 (mm) cc_final: 0.9088 (mt) REVERT: A 628 TYR cc_start: 0.8737 (m-80) cc_final: 0.8472 (m-10) REVERT: A 633 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: A 656 MET cc_start: 0.9004 (mtp) cc_final: 0.8782 (mtt) REVERT: A 735 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: A 755 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: A 784 PHE cc_start: 0.8523 (m-80) cc_final: 0.8121 (m-80) REVERT: A 1007 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4742 (tp) REVERT: A 1016 ARG cc_start: 0.7985 (ptp-170) cc_final: 0.7713 (ptm160) REVERT: A 1087 GLN cc_start: 0.8907 (mt0) cc_final: 0.8670 (mt0) REVERT: C 174 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7280 (ttmm) REVERT: C 215 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6737 (pp20) outliers start: 53 outliers final: 25 residues processed: 166 average time/residue: 0.6533 time to fit residues: 116.6019 Evaluate side-chains 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122447 restraints weight = 13445.810| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.46 r_work: 0.2776 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11917 Z= 0.158 Angle : 0.588 10.799 16272 Z= 0.314 Chirality : 0.041 0.189 1820 Planarity : 0.004 0.056 1873 Dihedral : 15.888 177.779 2121 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.98 % Allowed : 20.19 % Favored : 74.83 % 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: -0.59 (0.24), residues: 1252 helix: 0.61 (0.20), residues: 748 sheet: -2.06 (0.65), residues: 73 loop : -1.82 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.018 0.001 TYR A1046 PHE 0.011 0.001 PHE C 51 TRP 0.033 0.002 TRP C 137 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00356 (11917) covalent geometry : angle 0.58761 (16272) hydrogen bonds : bond 0.06109 ( 445) hydrogen bonds : angle 3.83000 ( 1274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: A 44 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7764 (tpp80) REVERT: A 65 GLN cc_start: 0.8426 (mt0) cc_final: 0.8138 (mm-40) REVERT: A 149 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7510 (ptm160) REVERT: A 177 LYS cc_start: 0.8807 (tptp) cc_final: 0.8580 (mtpt) REVERT: A 383 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 505 LEU cc_start: 0.9390 (mm) cc_final: 0.9152 (mt) REVERT: A 513 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 518 TYR cc_start: 0.8727 (m-80) cc_final: 0.8284 (m-80) REVERT: A 628 TYR cc_start: 0.8783 (m-80) cc_final: 0.8508 (m-10) REVERT: A 633 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 735 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: A 784 PHE cc_start: 0.8606 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1007 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4780 (tp) REVERT: A 1087 GLN cc_start: 0.8954 (mt0) cc_final: 0.8700 (mt0) REVERT: C 44 TYR cc_start: 0.8810 (t80) cc_final: 0.8483 (t80) REVERT: C 215 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6787 (pp20) outliers start: 59 outliers final: 34 residues processed: 177 average time/residue: 0.6097 time to fit residues: 116.0307 Evaluate side-chains 160 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 462 ASN A 622 ASN A 751 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.151448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122338 restraints weight = 13391.532| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.44 r_work: 0.2779 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11917 Z= 0.159 Angle : 0.586 10.795 16272 Z= 0.314 Chirality : 0.041 0.184 1820 Planarity : 0.004 0.055 1873 Dihedral : 15.826 178.089 2119 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.05 % Allowed : 21.88 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1252 helix: 0.72 (0.20), residues: 743 sheet: -2.08 (0.64), residues: 73 loop : -1.82 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.017 0.001 TYR A1046 PHE 0.010 0.001 PHE A 130 TRP 0.040 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00360 (11917) covalent geometry : angle 0.58558 (16272) hydrogen bonds : bond 0.06002 ( 445) hydrogen bonds : angle 3.83712 ( 1274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: A 44 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7769 (tpp80) REVERT: A 65 GLN cc_start: 0.8407 (mt0) cc_final: 0.8126 (mm-40) REVERT: A 111 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7697 (ttpp) REVERT: A 177 LYS cc_start: 0.8825 (tptp) cc_final: 0.8603 (mtpt) REVERT: A 383 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 505 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9154 (mt) REVERT: A 513 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 518 TYR cc_start: 0.8744 (m-80) cc_final: 0.8324 (m-80) REVERT: A 628 TYR cc_start: 0.8814 (m-80) cc_final: 0.8550 (m-10) REVERT: A 735 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: A 784 PHE cc_start: 0.8639 (m-80) cc_final: 0.8268 (m-80) REVERT: A 1007 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4750 (tp) REVERT: A 1087 GLN cc_start: 0.8935 (mt0) cc_final: 0.8671 (mt0) REVERT: C 44 TYR cc_start: 0.8829 (t80) cc_final: 0.8547 (t80) REVERT: C 144 GLU cc_start: 0.7739 (mp0) cc_final: 0.7411 (mp0) outliers start: 48 outliers final: 30 residues processed: 170 average time/residue: 0.6151 time to fit residues: 112.5452 Evaluate side-chains 158 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 124 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 462 ASN A 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127121 restraints weight = 13564.046| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.47 r_work: 0.2856 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11917 Z= 0.103 Angle : 0.519 9.663 16272 Z= 0.281 Chirality : 0.038 0.199 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.747 178.937 2119 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.12 % Allowed : 22.80 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1252 helix: 1.00 (0.20), residues: 731 sheet: -1.74 (0.69), residues: 66 loop : -1.76 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.011 0.001 TYR A1046 PHE 0.023 0.001 PHE A 459 TRP 0.042 0.002 TRP C 137 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00211 (11917) covalent geometry : angle 0.51922 (16272) hydrogen bonds : bond 0.04479 ( 445) hydrogen bonds : angle 3.62557 ( 1274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: A 44 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7781 (tpp80) REVERT: A 111 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7799 (ttpp) REVERT: A 149 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7481 (ttp-170) REVERT: A 383 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7788 (tp) REVERT: A 518 TYR cc_start: 0.8782 (m-80) cc_final: 0.8385 (m-80) REVERT: A 628 TYR cc_start: 0.8700 (m-80) cc_final: 0.8446 (m-10) REVERT: A 735 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: A 784 PHE cc_start: 0.8648 (m-80) cc_final: 0.8289 (m-80) REVERT: A 1007 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4572 (tp) REVERT: A 1087 GLN cc_start: 0.8834 (mt0) cc_final: 0.8629 (mt0) REVERT: C 144 GLU cc_start: 0.7742 (mp0) cc_final: 0.7515 (mp0) REVERT: C 165 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7881 (pp20) outliers start: 37 outliers final: 21 residues processed: 164 average time/residue: 0.6176 time to fit residues: 109.0681 Evaluate side-chains 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122941 restraints weight = 13269.233| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.40 r_work: 0.2781 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11917 Z= 0.160 Angle : 0.587 11.271 16272 Z= 0.311 Chirality : 0.041 0.189 1820 Planarity : 0.004 0.055 1873 Dihedral : 15.751 177.516 2119 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.46 % Allowed : 22.97 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1252 helix: 0.90 (0.20), residues: 737 sheet: -2.01 (0.65), residues: 73 loop : -1.73 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.018 0.001 TYR A1046 PHE 0.016 0.001 PHE A 459 TRP 0.032 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00366 (11917) covalent geometry : angle 0.58724 (16272) hydrogen bonds : bond 0.05795 ( 445) hydrogen bonds : angle 3.74284 ( 1274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: A 44 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7834 (tpp80) REVERT: A 97 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8768 (tttt) REVERT: A 111 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7602 (ttpp) REVERT: A 149 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7501 (ttp-170) REVERT: A 383 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 411 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8275 (ttpt) REVERT: A 518 TYR cc_start: 0.8758 (m-80) cc_final: 0.8333 (m-80) REVERT: A 628 TYR cc_start: 0.8776 (m-80) cc_final: 0.8516 (m-10) REVERT: A 735 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: A 784 PHE cc_start: 0.8669 (m-80) cc_final: 0.8289 (m-80) REVERT: A 788 GLU cc_start: 0.8209 (mp0) cc_final: 0.7921 (tp30) REVERT: A 849 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8280 (ttpt) REVERT: A 1007 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4675 (tp) REVERT: C 144 GLU cc_start: 0.7865 (mp0) cc_final: 0.7630 (mp0) REVERT: C 165 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7907 (pp20) outliers start: 41 outliers final: 26 residues processed: 149 average time/residue: 0.6281 time to fit residues: 100.6225 Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122718 restraints weight = 13478.687| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.47 r_work: 0.2784 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11917 Z= 0.147 Angle : 0.581 10.990 16272 Z= 0.308 Chirality : 0.041 0.184 1820 Planarity : 0.003 0.054 1873 Dihedral : 15.760 177.998 2119 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.21 % Allowed : 23.31 % Favored : 73.48 % 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: -0.23 (0.24), residues: 1252 helix: 0.95 (0.20), residues: 731 sheet: -2.00 (0.65), residues: 73 loop : -1.66 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.017 0.001 TYR A1046 PHE 0.016 0.001 PHE A 459 TRP 0.037 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00331 (11917) covalent geometry : angle 0.58065 (16272) hydrogen bonds : bond 0.05637 ( 445) hydrogen bonds : angle 3.70874 ( 1274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: A 44 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7864 (tpp80) REVERT: A 97 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8749 (tttm) REVERT: A 111 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7612 (ttpp) REVERT: A 149 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7501 (ttp-170) REVERT: A 383 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 411 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8273 (ttpt) REVERT: A 518 TYR cc_start: 0.8789 (m-80) cc_final: 0.8339 (m-80) REVERT: A 628 TYR cc_start: 0.8781 (m-80) cc_final: 0.8514 (m-10) REVERT: A 633 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: A 735 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8444 (mp10) REVERT: A 784 PHE cc_start: 0.8690 (m-80) cc_final: 0.8316 (m-80) REVERT: A 788 GLU cc_start: 0.8211 (mp0) cc_final: 0.7886 (tp30) REVERT: A 831 GLU cc_start: 0.8022 (tp30) cc_final: 0.7808 (mm-30) REVERT: A 849 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8262 (ttpt) REVERT: A 1007 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4646 (tp) REVERT: C 144 GLU cc_start: 0.7872 (mp0) cc_final: 0.7629 (mp0) REVERT: C 165 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7848 (pp20) outliers start: 38 outliers final: 25 residues processed: 149 average time/residue: 0.6244 time to fit residues: 100.1913 Evaluate side-chains 149 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 105 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128218 restraints weight = 13497.226| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.41 r_work: 0.2885 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11917 Z= 0.105 Angle : 0.525 9.958 16272 Z= 0.280 Chirality : 0.038 0.198 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.711 179.326 2119 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.62 % Allowed : 24.16 % Favored : 73.23 % 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: 0.07 (0.25), residues: 1252 helix: 1.23 (0.21), residues: 724 sheet: -1.72 (0.69), residues: 66 loop : -1.60 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.011 0.001 TYR C 67 PHE 0.016 0.001 PHE A 459 TRP 0.032 0.001 TRP C 137 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00224 (11917) covalent geometry : angle 0.52487 (16272) hydrogen bonds : bond 0.04224 ( 445) hydrogen bonds : angle 3.51644 ( 1274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.36 seconds wall clock time: 60 minutes 41.55 seconds (3641.55 seconds total)