Starting phenix.real_space_refine on Fri Sep 11 21:04:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrb_21366/09_2026/6vrb_21366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrb_21366/09_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_21366/09_2026/6vrb_21366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrb_21366/09_2026/6vrb_21366.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrb_21366/09_2026/6vrb_21366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrb_21366/09_2026/6vrb_21366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vrb_21366/09_2026/6vrb_21366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vrb_21366/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 52} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 30} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 2.55, per 1000 atoms: 0.22 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 515.0 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: 1.18 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: 2.01 Time building geometry restraints manager: 1.23 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: 14739 2.09 - 4.19: 1321 4.19 - 6.28: 159 6.28 - 8.37: 37 8.37 - 10.47: 16 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 - 16.40: 6321 16.40 - 32.81: 554 32.81 - 49.21: 180 49.21 - 65.62: 109 65.62 - 82.02: 26 Dihedral angle restraints: 7190 sinusoidal: 3415 harmonic: 3775 Sorted by residual: dihedral pdb=" C4' G B 15 " pdb=" C3' G B 15 " pdb=" C2' G B 15 " pdb=" C1' G B 15 " ideal model delta sinusoidal sigma weight residual 36.34 -39.37 75.71 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual 36.35 -39.33 75.68 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' U B 51 " pdb=" C3' U B 51 " pdb=" C2' U B 51 " pdb=" C1' U B 51 " ideal model delta sinusoidal sigma weight residual 36.34 -38.45 74.80 1 3.10e+00 1.04e-01 7.37e+02 ... (remaining 7187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1400 0.095 - 0.191: 315 0.191 - 0.286: 91 0.286 - 0.381: 13 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=" C3' U B 49 " pdb=" C4' U B 49 " pdb=" O3' U B 49 " pdb=" C2' U B 49 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3' U B 25 " pdb=" C4' U B 25 " pdb=" O3' U B 25 " pdb=" C2' U B 25 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-01 2.50e+01 3.02e+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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 1.261 10.467 16272 Z= 0.770 Chirality : 0.091 0.477 1820 Planarity : 0.006 0.067 1873 Dihedral : 16.264 82.019 4730 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/Z covalent geometry : bond 0.00911 / 0.54 (11917) covalent geometry : angle 1.26071 / 0.77 (16272) hydrogen bonds : bond 0.32656 / 16.94 ( 445) hydrogen bonds : angle 9.54248 / 3.80 ( 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 : 0.431 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: 0.6559 time to fit residues: 210.0389 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 : 0.369 ------------------------------------------------------------------------------- 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... A 101 HIS A 121 ASN A 127 ASN A 153 ASN 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.174678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151070 restraints weight = 13682.528| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.70 r_work: 0.3168 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11917 Z= 0.183 Angle : 1.017 16.775 16272 Z= 0.459 Chirality : 0.085 1.214 1820 Planarity : 0.005 0.062 1873 Dihedral : 15.449 151.428 1983 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.07 % Allowed : 17.15 % Favored : 77.79 % 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: -2.46 (0.22), residues: 1252 helix: -1.14 (0.18), residues: 728 sheet: -2.68 (0.63), residues: 73 loop : -2.06 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1016 TYR 0.027 0.002 TYR A1046 PHE 0.018 0.002 PHE A 130 TRP 0.016 0.002 TRP C 50 HIS 0.008 0.002 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (11917) covalent geometry : angle 1.01650 / 0.46 (16272) hydrogen bonds : bond 0.06849 / 3.52 ( 445) hydrogen bonds : angle 4.81012 / 1.99 ( 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 232 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.489 Fit side-chains REVERT: A 156 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7384 (tp40) REVERT: A 225 LEU cc_start: 0.7371 (mp) cc_final: 0.6973 (tt) REVERT: A 330 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8227 (ptp-170) REVERT: A 383 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7385 (tp) REVERT: A 667 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8528 (mtpt) REVERT: A 768 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 818 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 867 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: A 1017 ASN cc_start: 0.7711 (t0) cc_final: 0.7470 (m-40) REVERT: A 1087 GLN cc_start: 0.8338 (mt0) cc_final: 0.8119 (mt0) REVERT: C 17 ASN cc_start: 0.8345 (m-40) cc_final: 0.8124 (m110) REVERT: C 170 ILE cc_start: 0.8447 (tt) cc_final: 0.8011 (mt) REVERT: C 189 ILE cc_start: 0.7725 (mm) cc_final: 0.7524 (mm) REVERT: C 200 SER cc_start: 0.4917 (OUTLIER) cc_final: 0.4685 (p) outliers start: 60 outliers final: 12 residues processed: 215 average time/residue: 0.6623 time to fit residues: 153.2494 Evaluate side-chains 146 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 ARG Chi-restraints excluded: chain A residue 383 LEU 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 687 ILE Chi-restraints excluded: chain A residue 768 LEU 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 160 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 200 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 ASN A 462 ASN A 714 HIS A 751 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144688 restraints weight = 13649.874| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.56 r_work: 0.3096 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11917 Z= 0.130 Angle : 0.771 12.816 16272 Z= 0.358 Chirality : 0.066 0.765 1820 Planarity : 0.004 0.059 1873 Dihedral : 15.327 158.688 1983 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.90 % Allowed : 19.09 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1252 helix: -0.37 (0.19), residues: 736 sheet: -2.33 (0.65), residues: 72 loop : -1.99 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 296 TYR 0.014 0.001 TYR A 899 PHE 0.012 0.001 PHE A 548 TRP 0.018 0.001 TRP C 137 HIS 0.007 0.001 HIS A 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11917) covalent geometry : angle 0.77064 / 0.36 (16272) hydrogen bonds : bond 0.05095 / 2.61 ( 445) hydrogen bonds : angle 4.10233 / 1.70 ( 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 220 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.449 Fit side-chains REVERT: A 225 LEU cc_start: 0.7370 (mp) cc_final: 0.6961 (tt) REVERT: A 235 SER cc_start: 0.7166 (t) cc_final: 0.6749 (m) REVERT: A 287 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: A 383 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7281 (tp) REVERT: A 667 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8630 (mtpt) REVERT: A 710 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8298 (mp0) REVERT: A 858 ASP cc_start: 0.8218 (t0) cc_final: 0.7290 (t0) REVERT: A 1007 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4832 (tp) REVERT: A 1017 ASN cc_start: 0.7775 (t0) cc_final: 0.7460 (m-40) REVERT: A 1087 GLN cc_start: 0.8387 (mt0) cc_final: 0.8171 (mt0) REVERT: C 25 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 108 LYS cc_start: 0.8881 (mppt) cc_final: 0.8340 (mtpp) REVERT: C 170 ILE cc_start: 0.8344 (tt) cc_final: 0.7782 (mt) outliers start: 58 outliers final: 18 residues processed: 202 average time/residue: 0.6546 time to fit residues: 142.6731 Evaluate side-chains 149 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 287 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 656 MET Chi-restraints excluded: chain A residue 667 LYS 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 857 TYR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 333 ASN 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 = 0.3846 r_free = 0.3846 target = 0.165240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137248 restraints weight = 13472.145| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.38 r_work: 0.2993 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11917 Z= 0.135 Angle : 0.751 12.176 16272 Z= 0.352 Chirality : 0.063 0.678 1820 Planarity : 0.004 0.057 1873 Dihedral : 15.224 161.662 1981 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.15 % Allowed : 19.51 % Favored : 75.34 % 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: -1.00 (0.24), residues: 1252 helix: 0.21 (0.20), residues: 742 sheet: -2.31 (0.66), residues: 70 loop : -1.81 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 330 TYR 0.014 0.001 TYR C 162 PHE 0.016 0.001 PHE A 459 TRP 0.026 0.002 TRP C 137 HIS 0.005 0.001 HIS A 870 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11917) covalent geometry : angle 0.75105 / 0.35 (16272) hydrogen bonds : bond 0.05228 / 2.68 ( 445) hydrogen bonds : angle 3.82256 / 1.60 ( 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 204 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: A 65 GLN cc_start: 0.8195 (mt0) cc_final: 0.7900 (mm-40) REVERT: A 132 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7502 (ptpt) REVERT: A 225 LEU cc_start: 0.7325 (mp) cc_final: 0.6882 (tt) REVERT: A 237 SER cc_start: 0.9120 (t) cc_final: 0.8915 (m) REVERT: A 238 GLU cc_start: 0.8376 (tp30) cc_final: 0.8087 (mp0) REVERT: A 246 THR cc_start: 0.8604 (p) cc_final: 0.8293 (p) REVERT: A 383 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7391 (tp) REVERT: A 586 GLN cc_start: 0.8619 (mt0) cc_final: 0.8289 (mm110) REVERT: A 667 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8635 (mtpt) REVERT: A 784 PHE cc_start: 0.8170 (m-80) cc_final: 0.7830 (m-80) REVERT: A 1007 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4757 (tp) REVERT: A 1087 GLN cc_start: 0.8693 (mt0) cc_final: 0.8476 (mt0) REVERT: C 25 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: C 41 ARG cc_start: 0.7404 (pmm150) cc_final: 0.7096 (pmm150) REVERT: C 82 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7949 (tp30) outliers start: 61 outliers final: 21 residues processed: 186 average time/residue: 0.6609 time to fit residues: 132.1547 Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 112 ILE 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 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 656 MET 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 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1046 TYR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 25 GLU 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 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 5.9990 chunk 118 optimal weight: 0.0170 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.0738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN A 410 HIS A 462 ASN A 751 GLN A 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134140 restraints weight = 13377.767| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.30 r_work: 0.2957 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11917 Z= 0.138 Angle : 0.731 12.380 16272 Z= 0.343 Chirality : 0.062 0.626 1820 Planarity : 0.003 0.057 1873 Dihedral : 15.336 161.161 1979 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.05 % Allowed : 21.96 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1252 helix: 0.51 (0.20), residues: 750 sheet: -2.21 (0.64), residues: 72 loop : -1.80 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 384 TYR 0.013 0.001 TYR A 596 PHE 0.011 0.001 PHE A 459 TRP 0.021 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11917) covalent geometry : angle 0.73138 / 0.34 (16272) hydrogen bonds : bond 0.05142 / 2.63 ( 445) hydrogen bonds : angle 3.71803 / 1.56 ( 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 193 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: A 132 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7565 (ptpt) REVERT: A 149 ARG cc_start: 0.7759 (ptm160) cc_final: 0.7473 (ptm160) REVERT: A 238 GLU cc_start: 0.8403 (tp30) cc_final: 0.8127 (mp0) REVERT: A 383 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (tp) REVERT: A 466 LYS cc_start: 0.8396 (ptpt) cc_final: 0.7936 (mtmt) REVERT: A 586 GLN cc_start: 0.8639 (mt0) cc_final: 0.8363 (mm110) REVERT: A 633 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: A 667 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8625 (mtpt) REVERT: A 735 GLN cc_start: 0.8464 (mt0) cc_final: 0.8256 (mp10) REVERT: A 784 PHE cc_start: 0.8416 (m-80) cc_final: 0.8106 (m-80) REVERT: A 875 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: A 1007 LEU cc_start: 0.5019 (OUTLIER) cc_final: 0.4334 (tp) REVERT: A 1087 GLN cc_start: 0.8751 (mt0) cc_final: 0.8529 (mt0) REVERT: C 25 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8312 (mm-30) outliers start: 48 outliers final: 21 residues processed: 180 average time/residue: 0.6386 time to fit residues: 123.7429 Evaluate side-chains 153 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 112 ILE 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 594 MET 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 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 875 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 35 GLU 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 160 LEU Chi-restraints excluded: chain C residue 192 GLU 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: 0.9990 chunk 103 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132017 restraints weight = 13403.873| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.33 r_work: 0.2916 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11917 Z= 0.145 Angle : 0.744 12.054 16272 Z= 0.348 Chirality : 0.064 0.680 1820 Planarity : 0.003 0.056 1873 Dihedral : 15.400 158.458 1979 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.73 % Allowed : 21.96 % Favored : 73.31 % 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: -0.43 (0.24), residues: 1252 helix: 0.72 (0.20), residues: 752 sheet: -2.04 (0.67), residues: 72 loop : -1.73 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.024 0.001 TYR A1046 PHE 0.010 0.001 PHE A 459 TRP 0.029 0.002 TRP C 137 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11917) covalent geometry : angle 0.74380 / 0.35 (16272) hydrogen bonds : bond 0.05334 / 2.73 ( 445) hydrogen bonds : angle 3.67318 / 1.53 ( 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 194 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: A 44 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7785 (tpp80) REVERT: A 149 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7649 (ptm160) REVERT: A 238 GLU cc_start: 0.8451 (tp30) cc_final: 0.8196 (mp0) REVERT: A 246 THR cc_start: 0.8935 (p) cc_final: 0.8680 (p) REVERT: A 355 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6758 (m-40) REVERT: A 383 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 466 LYS cc_start: 0.8367 (ptpt) cc_final: 0.7918 (mtmt) REVERT: A 513 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.8859 (t) REVERT: A 628 TYR cc_start: 0.8737 (m-80) cc_final: 0.8476 (m-10) REVERT: A 633 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: A 667 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: A 735 GLN cc_start: 0.8571 (mt0) cc_final: 0.8365 (mt0) REVERT: A 784 PHE cc_start: 0.8531 (m-80) cc_final: 0.8070 (m-80) REVERT: A 1007 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4279 (tp) REVERT: A 1087 GLN cc_start: 0.8856 (mt0) cc_final: 0.8629 (mt0) REVERT: C 160 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8497 (mt) outliers start: 56 outliers final: 21 residues processed: 176 average time/residue: 0.6335 time to fit residues: 119.9720 Evaluate side-chains 150 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 355 ASN 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 513 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 623 LYS 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 798 VAL 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 1007 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 VAL 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 160 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 410 HIS A 462 ASN A 586 GLN A 622 ASN A 751 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124203 restraints weight = 13261.632| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.55 r_work: 0.2842 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11917 Z= 0.184 Angle : 0.815 11.682 16272 Z= 0.378 Chirality : 0.071 0.856 1820 Planarity : 0.004 0.055 1873 Dihedral : 15.530 154.747 1979 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.56 % Allowed : 21.96 % 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: -0.46 (0.24), residues: 1252 helix: 0.73 (0.20), residues: 742 sheet: -2.06 (0.67), residues: 73 loop : -1.77 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 202 TYR 0.018 0.001 TYR A1046 PHE 0.012 0.002 PHE C 51 TRP 0.025 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (11917) covalent geometry : angle 0.81538 / 0.38 (16272) hydrogen bonds : bond 0.06358 / 3.26 ( 445) hydrogen bonds : angle 3.83567 / 1.59 ( 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 185 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: A 44 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7801 (tpp80) REVERT: A 132 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7632 (ptpp) REVERT: A 355 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6706 (m-40) REVERT: A 383 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 466 LYS cc_start: 0.8483 (ptpt) cc_final: 0.7912 (mtmt) REVERT: A 505 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9128 (mt) REVERT: A 513 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.8842 (t) REVERT: A 518 TYR cc_start: 0.8728 (m-80) cc_final: 0.8259 (m-80) REVERT: A 586 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8225 (mm110) REVERT: A 626 LYS cc_start: 0.8644 (pptt) cc_final: 0.8323 (ptmm) REVERT: A 628 TYR cc_start: 0.8867 (m-80) cc_final: 0.8590 (m-10) REVERT: A 667 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8668 (mtpt) REVERT: A 735 GLN cc_start: 0.8722 (mt0) cc_final: 0.8508 (mt0) REVERT: A 784 PHE cc_start: 0.8619 (m-80) cc_final: 0.8192 (m-80) REVERT: A 798 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7505 (t) REVERT: A 825 VAL cc_start: 0.8968 (t) cc_final: 0.8612 (m) REVERT: A 1007 LEU cc_start: 0.4714 (OUTLIER) cc_final: 0.4440 (tp) REVERT: A 1087 GLN cc_start: 0.8937 (mt0) cc_final: 0.8632 (mt0) REVERT: C 44 TYR cc_start: 0.8644 (t80) cc_final: 0.8207 (t80) REVERT: C 144 GLU cc_start: 0.7815 (mp0) cc_final: 0.7575 (mp0) outliers start: 54 outliers final: 27 residues processed: 169 average time/residue: 0.6397 time to fit residues: 116.7202 Evaluate side-chains 153 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 355 ASN 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 505 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 621 LEU 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 780 TRP Chi-restraints excluded: chain A residue 798 VAL 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 1055 SER 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 82 GLU 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 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: 6.9990 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3753 r_free = 0.3753 target = 0.156867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128852 restraints weight = 13407.458| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.32 r_work: 0.2882 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11917 Z= 0.151 Angle : 0.766 12.095 16272 Z= 0.356 Chirality : 0.066 0.771 1820 Planarity : 0.003 0.054 1873 Dihedral : 15.567 157.733 1979 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.72 % Allowed : 23.14 % Favored : 73.14 % 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: -0.32 (0.24), residues: 1252 helix: 0.85 (0.20), residues: 745 sheet: -2.01 (0.67), residues: 73 loop : -1.73 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 202 TYR 0.015 0.001 TYR A1046 PHE 0.010 0.001 PHE A 130 TRP 0.033 0.002 TRP C 137 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (11917) covalent geometry : angle 0.76645 / 0.36 (16272) hydrogen bonds : bond 0.05500 / 2.82 ( 445) hydrogen bonds : angle 3.72860 / 1.54 ( 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 178 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: A 44 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7877 (tpp80) REVERT: A 355 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6656 (m-40) REVERT: A 383 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7859 (tp) REVERT: A 466 LYS cc_start: 0.8442 (ptpt) cc_final: 0.7897 (mtmt) REVERT: A 513 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8819 (t) REVERT: A 586 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8196 (mm110) REVERT: A 626 LYS cc_start: 0.8561 (pptt) cc_final: 0.8212 (ptmm) REVERT: A 628 TYR cc_start: 0.8786 (m-80) cc_final: 0.8528 (m-10) REVERT: A 667 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (mtpt) REVERT: A 735 GLN cc_start: 0.8629 (mt0) cc_final: 0.8420 (mt0) REVERT: A 784 PHE cc_start: 0.8644 (m-80) cc_final: 0.8214 (m-80) REVERT: A 825 VAL cc_start: 0.8959 (t) cc_final: 0.8587 (m) REVERT: A 1007 LEU cc_start: 0.4739 (OUTLIER) cc_final: 0.4482 (tp) REVERT: A 1087 GLN cc_start: 0.8896 (mt0) cc_final: 0.8681 (mt0) REVERT: C 44 TYR cc_start: 0.8675 (t80) cc_final: 0.8255 (t80) REVERT: C 144 GLU cc_start: 0.7789 (mp0) cc_final: 0.7485 (mp0) REVERT: C 160 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8501 (mt) outliers start: 44 outliers final: 22 residues processed: 166 average time/residue: 0.6101 time to fit residues: 109.5123 Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 355 ASN 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 513 SER Chi-restraints excluded: chain A residue 594 MET 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 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 1007 LEU Chi-restraints excluded: chain A residue 1055 SER 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 82 GLU 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 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 70 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 462 ASN A 751 GLN A1017 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136342 restraints weight = 13366.975| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.19 r_work: 0.3028 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 0.049 11917 Z= 0.112 Angle : 0.687 12.799 16272 Z= 0.318 Chirality : 0.058 0.517 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.481 162.755 1979 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.28 % Allowed : 24.92 % Favored : 72.80 % 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: -0.02 (0.25), residues: 1252 helix: 1.12 (0.20), residues: 736 sheet: -1.92 (0.68), residues: 70 loop : -1.61 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 202 TYR 0.015 0.001 TYR A1046 PHE 0.010 0.001 PHE A 459 TRP 0.035 0.001 TRP C 137 HIS 0.002 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (11917) covalent geometry : angle 0.68742 / 0.32 (16272) hydrogen bonds : bond 0.04160 / 2.13 ( 445) hydrogen bonds : angle 3.52533 / 1.46 ( 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 169 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: A 44 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7859 (tpp80) REVERT: A 383 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7595 (tp) REVERT: A 466 LYS cc_start: 0.8402 (ptpt) cc_final: 0.7885 (mtmt) REVERT: A 586 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8074 (mm110) REVERT: A 667 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8540 (mtpt) REVERT: A 735 GLN cc_start: 0.8432 (mt0) cc_final: 0.8224 (mt0) REVERT: A 784 PHE cc_start: 0.8650 (m-80) cc_final: 0.8272 (m-80) REVERT: A 819 ASN cc_start: 0.7936 (m110) cc_final: 0.7736 (m-40) REVERT: A 824 LEU cc_start: 0.9258 (tm) cc_final: 0.9000 (tp) REVERT: A 1016 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7594 (ptp-170) REVERT: A 1119 MET cc_start: 0.8498 (ttp) cc_final: 0.8285 (ttm) REVERT: C 44 TYR cc_start: 0.8636 (t80) cc_final: 0.8182 (t80) REVERT: C 144 GLU cc_start: 0.7739 (mp0) cc_final: 0.7464 (mp0) REVERT: C 160 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8324 (mt) outliers start: 27 outliers final: 11 residues processed: 160 average time/residue: 0.6349 time to fit residues: 109.8515 Evaluate side-chains 142 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 667 LYS 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 C residue 35 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU 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 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 462 ASN A 751 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130677 restraints weight = 13476.603| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.32 r_work: 0.2883 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11917 Z= 0.151 Angle : 0.755 11.628 16272 Z= 0.351 Chirality : 0.064 0.703 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.469 158.823 1979 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.20 % Allowed : 25.17 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1252 helix: 1.07 (0.20), residues: 737 sheet: -1.93 (0.67), residues: 72 loop : -1.62 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 202 TYR 0.017 0.001 TYR C 67 PHE 0.010 0.001 PHE C 51 TRP 0.032 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11917) covalent geometry : angle 0.75523 / 0.35 (16272) hydrogen bonds : bond 0.05420 / 2.78 ( 445) hydrogen bonds : angle 3.65535 / 1.51 ( 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 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: A 44 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7937 (tpp80) REVERT: A 383 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7739 (tp) REVERT: A 586 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8168 (mm110) REVERT: A 626 LYS cc_start: 0.8572 (pptt) cc_final: 0.8195 (ptmm) REVERT: A 628 TYR cc_start: 0.8747 (m-80) cc_final: 0.8512 (m-10) REVERT: A 667 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (mtpt) REVERT: A 735 GLN cc_start: 0.8654 (mt0) cc_final: 0.8426 (mt0) REVERT: A 784 PHE cc_start: 0.8659 (m-80) cc_final: 0.8282 (m-80) REVERT: C 41 ARG cc_start: 0.7547 (pmt170) cc_final: 0.6768 (pmm150) REVERT: C 44 TYR cc_start: 0.8682 (t80) cc_final: 0.8274 (t80) REVERT: C 144 GLU cc_start: 0.7770 (mp0) cc_final: 0.7516 (mp0) REVERT: C 160 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8356 (mt) outliers start: 26 outliers final: 10 residues processed: 144 average time/residue: 0.6278 time to fit residues: 97.5012 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 667 LYS Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU 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: 0.6980 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 0.0010 chunk 32 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 324 GLN A 462 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135004 restraints weight = 13503.517| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.28 r_work: 0.2988 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11917 Z= 0.118 Angle : 0.699 12.632 16272 Z= 0.324 Chirality : 0.058 0.548 1820 Planarity : 0.003 0.054 1873 Dihedral : 15.480 163.096 1979 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.69 % Allowed : 26.01 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1252 helix: 1.24 (0.20), residues: 736 sheet: -1.93 (0.67), residues: 70 loop : -1.54 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.014 0.001 TYR C 67 PHE 0.011 0.001 PHE A 169 TRP 0.031 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11917) covalent geometry : angle 0.69876 / 0.32 (16272) hydrogen bonds : bond 0.04367 / 2.24 ( 445) hydrogen bonds : angle 3.52778 / 1.46 ( 1274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3619.02 seconds wall clock time: 62 minutes 37.62 seconds (3757.62 seconds total)