Starting phenix.real_space_refine on Tue Jul 29 19:53:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrb_21366/07_2025/6vrb_21366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrb_21366/07_2025/6vrb_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_21366/07_2025/6vrb_21366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrb_21366/07_2025/6vrb_21366.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrb_21366/07_2025/6vrb_21366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrb_21366/07_2025/6vrb_21366.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 37 5.16 5 C 7210 2.51 5 N 1948 2.21 5 O 2335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11581 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1093 Classifications: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 30} Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8574 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 23, 'TRANS': 1007} Chain breaks: 2 Chain: "C" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1914 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Time building chain proxies: 7.21, per 1000 atoms: 0.62 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.45 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: 3.64 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1871 1.32 - 1.44: 3397 1.44 - 1.56: 6486 1.56 - 1.69: 102 1.69 - 1.81: 61 Bond restraints: 11917 Sorted by residual: bond pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" N ILE A 170 " pdb=" CA ILE A 170 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.51e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14894 2.09 - 4.19: 1210 4.19 - 6.28: 119 6.28 - 8.37: 35 8.37 - 10.47: 14 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N GLU A 431 " pdb=" CA GLU A 431 " pdb=" C GLU A 431 " ideal model delta sigma weight residual 114.62 105.17 9.45 1.14e+00 7.69e-01 6.87e+01 angle pdb=" N VAL A 595 " pdb=" CA VAL A 595 " pdb=" C VAL A 595 " ideal model delta sigma weight residual 110.72 104.95 5.77 1.01e+00 9.80e-01 3.27e+01 angle pdb=" N LYS C 65 " pdb=" CA LYS C 65 " pdb=" C LYS C 65 " ideal model delta sigma weight residual 111.02 117.58 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ARG A 316 " pdb=" N ASN A 317 " pdb=" CA ASN A 317 " ideal model delta sigma weight residual 120.28 127.07 -6.79 1.34e+00 5.57e-01 2.57e+01 angle pdb=" C THR A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta sigma weight residual 121.19 128.99 -7.80 1.59e+00 3.96e-01 2.41e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7102 35.54 - 71.09: 206 71.09 - 106.63: 20 106.63 - 142.17: 0 142.17 - 177.71: 4 Dihedral angle restraints: 7332 sinusoidal: 3557 harmonic: 3775 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 232.00 54.29 177.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 37 " pdb=" C1' U B 37 " pdb=" N1 U B 37 " pdb=" C2 U B 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.39 -177.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 51 " pdb=" C1' U B 51 " pdb=" N1 U B 51 " pdb=" C2 U B 51 " ideal model delta sinusoidal sigma weight residual 232.00 58.11 173.89 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1486 0.095 - 0.191: 289 0.191 - 0.286: 43 0.286 - 0.381: 1 0.381 - 0.477: 1 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA LYS C 11 " pdb=" N LYS C 11 " pdb=" C LYS C 11 " pdb=" CB LYS C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN A 532 " pdb=" N ASN A 532 " pdb=" C ASN A 532 " pdb=" CB ASN A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL A 527 " pdb=" CA VAL A 527 " pdb=" CG1 VAL A 527 " pdb=" CG2 VAL A 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1817 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 5 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE C 5 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE C 5 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 508 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN A 508 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN A 508 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 509 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C MET A 594 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 595 " 0.018 2.00e-02 2.50e+03 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 60 2.48 - 3.09: 7248 3.09 - 3.69: 17273 3.69 - 4.30: 26170 4.30 - 4.90: 41661 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG A 212 " pdb=" OG SER A 213 " model vdw 1.877 3.040 nonbonded pdb=" OH TYR C 197 " pdb=" OH TYR C 213 " model vdw 2.166 3.040 nonbonded pdb=" O TYR C 197 " pdb=" O SER C 200 " model vdw 2.178 3.040 nonbonded pdb=" O6 G B 1 " pdb=" O ASN A 309 " model vdw 2.216 3.040 nonbonded pdb=" O2' G B 15 " pdb=" NH1 ARG A 129 " model vdw 2.231 3.120 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 11917 Z= 0.538 Angle : 1.205 10.467 16272 Z= 0.768 Chirality : 0.076 0.477 1820 Planarity : 0.006 0.067 1873 Dihedral : 16.053 177.714 4872 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.12 % Allowed : 8.95 % Favored : 87.92 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.004 TRP C 64 HIS 0.013 0.002 HIS A 74 PHE 0.042 0.003 PHE C 63 TYR 0.030 0.003 TYR A1046 ARG 0.017 0.002 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.32656 ( 445) hydrogen bonds : angle 9.54248 ( 1274) covalent geometry : bond 0.00907 (11917) covalent geometry : angle 1.20495 (16272) *********************** 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 : 1.460 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: 1.2766 time to fit residues: 409.6913 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 : 1.295 ------------------------------------------------------------------------------- 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 109 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 118 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 ASN A 127 ASN A 153 ASN A 165 GLN A 285 ASN A 289 ASN A 329 HIS A 333 ASN A 532 ASN A 576 ASN A 598 GLN A 654 GLN A 714 HIS A 751 GLN A 772 ASN A 866 GLN A 915 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1111 GLN C 129 HIS C 180 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.174400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147469 restraints weight = 13715.976| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.00 r_work: 0.3152 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11917 Z= 0.141 Angle : 0.646 9.846 16272 Z= 0.351 Chirality : 0.041 0.195 1820 Planarity : 0.005 0.060 1873 Dihedral : 16.248 178.252 2125 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.98 % Allowed : 16.64 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1252 helix: -1.26 (0.18), residues: 735 sheet: -2.51 (0.64), residues: 72 loop : -2.07 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 50 HIS 0.005 0.001 HIS C 129 PHE 0.014 0.002 PHE C 63 TYR 0.024 0.002 TYR A1046 ARG 0.004 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05822 ( 445) hydrogen bonds : angle 4.73290 ( 1274) covalent geometry : bond 0.00292 (11917) covalent geometry : angle 0.64552 (16272) *********************** 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 243 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.238 Fit side-chains REVERT: A 225 LEU cc_start: 0.7491 (mp) cc_final: 0.6952 (tt) REVERT: A 235 SER cc_start: 0.7272 (t) cc_final: 0.6891 (m) REVERT: A 280 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: A 281 GLU cc_start: 0.8671 (mp0) cc_final: 0.8433 (pm20) REVERT: A 330 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8176 (ptp-170) REVERT: A 383 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7170 (tp) REVERT: A 667 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8614 (mtpt) REVERT: A 768 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 818 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 867 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: A 935 ASP cc_start: 0.8224 (m-30) cc_final: 0.7970 (m-30) REVERT: A 1017 ASN cc_start: 0.7673 (t0) cc_final: 0.7381 (m-40) REVERT: A 1087 GLN cc_start: 0.8300 (mt0) cc_final: 0.8095 (mt0) REVERT: C 17 ASN cc_start: 0.8310 (m-40) cc_final: 0.8084 (m110) REVERT: C 19 MET cc_start: 0.8462 (mmt) cc_final: 0.8210 (mmt) REVERT: C 170 ILE cc_start: 0.8361 (tt) cc_final: 0.7961 (mt) outliers start: 59 outliers final: 11 residues processed: 228 average time/residue: 1.4125 time to fit residues: 345.5908 Evaluate side-chains 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 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 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 0.0020 chunk 81 optimal weight: 4.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 333 ASN A 357 ASN A 410 HIS A 462 ASN A 714 HIS A 735 GLN A 751 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129677 restraints weight = 13405.106| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.76 r_work: 0.2859 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4929 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= 0.151 Angle : 0.624 11.003 16272 Z= 0.335 Chirality : 0.042 0.190 1820 Planarity : 0.004 0.059 1873 Dihedral : 16.013 177.538 2123 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.25 % Allowed : 17.91 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.23), residues: 1252 helix: -0.45 (0.19), residues: 744 sheet: -2.45 (0.64), residues: 72 loop : -1.94 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 137 HIS 0.006 0.002 HIS A 714 PHE 0.013 0.002 PHE A 130 TYR 0.024 0.002 TYR A1046 ARG 0.007 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.06242 ( 445) hydrogen bonds : angle 4.06127 ( 1274) covalent geometry : bond 0.00328 (11917) covalent geometry : angle 0.62384 (16272) *********************** 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 242 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: A 54 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8901 (t0) REVERT: A 65 GLN cc_start: 0.8325 (mt0) cc_final: 0.7995 (mm-40) REVERT: A 132 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7573 (ptpt) REVERT: A 156 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7791 (tp40) REVERT: A 238 GLU cc_start: 0.8451 (tp30) cc_final: 0.8248 (mp0) REVERT: A 246 THR cc_start: 0.8563 (p) cc_final: 0.8206 (p) REVERT: A 266 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8648 (ptpt) REVERT: A 351 GLU cc_start: 0.7860 (pm20) cc_final: 0.7520 (tm-30) REVERT: A 383 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 499 LEU cc_start: 0.8570 (mt) cc_final: 0.8308 (mt) REVERT: A 586 GLN cc_start: 0.8713 (mt0) cc_final: 0.8429 (mm110) REVERT: A 784 PHE cc_start: 0.8123 (m-80) cc_final: 0.7804 (m-80) REVERT: A 858 ASP cc_start: 0.8294 (t0) cc_final: 0.8090 (t0) REVERT: A 1007 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4623 (tp) REVERT: A 1087 GLN cc_start: 0.8795 (mt0) cc_final: 0.8511 (mt0) REVERT: C 19 MET cc_start: 0.8739 (mmt) cc_final: 0.8439 (mmt) REVERT: C 25 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: C 208 TYR cc_start: 0.7199 (t80) cc_final: 0.6719 (t80) outliers start: 74 outliers final: 20 residues processed: 221 average time/residue: 1.3885 time to fit residues: 330.1710 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 54 ASN 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 266 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 448 ILE Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 35 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 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 360 GLN A 410 HIS A 462 ASN A 751 GLN A 793 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.156957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127499 restraints weight = 13327.985| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.48 r_work: 0.2847 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11917 Z= 0.137 Angle : 0.581 11.450 16272 Z= 0.313 Chirality : 0.041 0.193 1820 Planarity : 0.004 0.058 1873 Dihedral : 15.920 178.253 2121 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.41 % Allowed : 20.44 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1252 helix: 0.15 (0.20), residues: 743 sheet: -2.41 (0.64), residues: 73 loop : -1.87 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 137 HIS 0.004 0.001 HIS C 72 PHE 0.011 0.001 PHE A 130 TYR 0.018 0.001 TYR A1046 ARG 0.005 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 445) hydrogen bonds : angle 3.83592 ( 1274) covalent geometry : bond 0.00300 (11917) covalent geometry : angle 0.58082 (16272) *********************** 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 198 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 134 time to evaluate : 1.311 Fit side-chains REVERT: A 41 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 65 GLN cc_start: 0.8387 (mt0) cc_final: 0.8106 (mm-40) REVERT: A 132 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7560 (ptpt) REVERT: A 149 ARG cc_start: 0.7730 (ptm160) cc_final: 0.7486 (ptm160) REVERT: A 177 LYS cc_start: 0.8586 (tptp) cc_final: 0.8376 (tppt) REVERT: A 246 THR cc_start: 0.8799 (p) cc_final: 0.8495 (p) REVERT: A 383 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7587 (tp) REVERT: A 586 GLN cc_start: 0.8704 (mt0) cc_final: 0.8425 (mm110) REVERT: A 633 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 784 PHE cc_start: 0.8403 (m-80) cc_final: 0.7991 (m-80) REVERT: A 1007 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4270 (tp) REVERT: C 19 MET cc_start: 0.8743 (mmt) cc_final: 0.8514 (mmt) REVERT: C 139 LYS cc_start: 0.8425 (tptp) cc_final: 0.8197 (tptp) REVERT: C 165 GLU cc_start: 0.7909 (mp0) cc_final: 0.7643 (pm20) REVERT: C 174 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7342 (ttmm) outliers start: 64 outliers final: 26 residues processed: 182 average time/residue: 1.3448 time to fit residues: 263.7211 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 254 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 623 LYS Chi-restraints excluded: chain A residue 633 GLN 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 836 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127480 restraints weight = 13318.387| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.45 r_work: 0.2856 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11917 Z= 0.127 Angle : 0.551 10.998 16272 Z= 0.297 Chirality : 0.040 0.191 1820 Planarity : 0.003 0.056 1873 Dihedral : 15.874 178.049 2121 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.31 % Allowed : 21.79 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1252 helix: 0.52 (0.20), residues: 745 sheet: -2.24 (0.65), residues: 72 loop : -1.84 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 PHE 0.009 0.001 PHE C 91 TYR 0.018 0.001 TYR A1046 ARG 0.004 0.000 ARG A 881 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 445) hydrogen bonds : angle 3.74433 ( 1274) covalent geometry : bond 0.00273 (11917) covalent geometry : angle 0.55060 (16272) *********************** 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 189 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: A 65 GLN cc_start: 0.8362 (mt0) cc_final: 0.8085 (mm-40) REVERT: A 132 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7556 (ptpt) REVERT: A 149 ARG cc_start: 0.7857 (ptm160) cc_final: 0.7620 (ptm160) REVERT: A 177 LYS cc_start: 0.8717 (tptp) cc_final: 0.8456 (tppt) REVERT: A 225 LEU cc_start: 0.7307 (mp) cc_final: 0.6848 (tt) REVERT: A 246 THR cc_start: 0.8928 (p) cc_final: 0.8566 (p) REVERT: A 383 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7616 (tp) REVERT: A 586 GLN cc_start: 0.8665 (mt0) cc_final: 0.8362 (mm110) REVERT: A 633 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 755 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: A 784 PHE cc_start: 0.8419 (m-80) cc_final: 0.7982 (m-80) REVERT: A 853 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.7622 (tmtm) REVERT: A 1007 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.4330 (tp) REVERT: C 19 MET cc_start: 0.8746 (mmt) cc_final: 0.8523 (mmt) REVERT: C 165 GLU cc_start: 0.7945 (mp0) cc_final: 0.7660 (pm20) REVERT: C 174 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7226 (ttmm) REVERT: C 215 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6654 (pp20) outliers start: 51 outliers final: 22 residues processed: 175 average time/residue: 1.4123 time to fit residues: 265.7953 Evaluate side-chains 144 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 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 633 GLN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain C residue 35 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 174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 165 GLN A 410 HIS A 462 ASN 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 = 0.3685 r_free = 0.3685 target = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121671 restraints weight = 13468.287| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.51 r_work: 0.2759 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11917 Z= 0.186 Angle : 0.621 12.023 16272 Z= 0.330 Chirality : 0.042 0.186 1820 Planarity : 0.004 0.057 1873 Dihedral : 15.903 178.238 2121 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.14 % Allowed : 21.54 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1252 helix: 0.50 (0.20), residues: 751 sheet: -2.16 (0.64), residues: 73 loop : -1.82 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 PHE 0.011 0.002 PHE C 51 TYR 0.019 0.001 TYR A1046 ARG 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.06509 ( 445) hydrogen bonds : angle 3.85722 ( 1274) covalent geometry : bond 0.00426 (11917) covalent geometry : angle 0.62086 (16272) *********************** 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 175 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: A 65 GLN cc_start: 0.8439 (mt0) cc_final: 0.8153 (mm-40) REVERT: A 101 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8658 (t-170) REVERT: A 116 ASP cc_start: 0.7675 (m-30) cc_final: 0.7126 (m-30) REVERT: A 177 LYS cc_start: 0.8802 (tptp) cc_final: 0.8515 (mtpt) REVERT: A 246 THR cc_start: 0.9156 (p) cc_final: 0.8879 (p) REVERT: A 383 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (tp) REVERT: A 513 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.8822 (t) REVERT: A 628 TYR cc_start: 0.8779 (m-80) cc_final: 0.8503 (m-10) REVERT: A 633 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 638 MET cc_start: 0.9312 (ttt) cc_final: 0.8984 (ttt) REVERT: A 784 PHE cc_start: 0.8545 (m-80) cc_final: 0.8141 (m-80) REVERT: A 1016 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7622 (ptp-170) REVERT: C 19 MET cc_start: 0.8866 (mmt) cc_final: 0.8641 (mmt) REVERT: C 162 TYR cc_start: 0.8060 (t80) cc_final: 0.7734 (t80) REVERT: C 165 GLU cc_start: 0.7949 (mp0) cc_final: 0.7641 (pm20) REVERT: C 174 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7393 (ttmm) REVERT: C 215 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6725 (pp20) outliers start: 49 outliers final: 22 residues processed: 163 average time/residue: 1.4671 time to fit residues: 257.9110 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 101 HIS 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 493 ASP 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 633 GLN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126687 restraints weight = 13631.161| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.69 r_work: 0.2836 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11917 Z= 0.107 Angle : 0.523 10.226 16272 Z= 0.282 Chirality : 0.039 0.197 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.812 178.810 2121 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.12 % Allowed : 23.06 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1252 helix: 0.89 (0.20), residues: 744 sheet: -1.73 (0.69), residues: 66 loop : -1.81 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 PHE 0.010 0.001 PHE C 91 TYR 0.016 0.001 TYR A1046 ARG 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 445) hydrogen bonds : angle 3.59299 ( 1274) covalent geometry : bond 0.00222 (11917) covalent geometry : angle 0.52322 (16272) *********************** 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 170 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: A 44 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7737 (tpp80) REVERT: A 101 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8717 (t-170) REVERT: A 149 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7523 (ttp-170) REVERT: A 246 THR cc_start: 0.9018 (p) cc_final: 0.8757 (p) REVERT: A 383 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 586 GLN cc_start: 0.8622 (tp40) cc_final: 0.8248 (mm110) REVERT: A 628 TYR cc_start: 0.8730 (m-80) cc_final: 0.8478 (m-10) REVERT: A 784 PHE cc_start: 0.8595 (m-80) cc_final: 0.8193 (m-80) REVERT: A 798 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7418 (t) REVERT: C 165 GLU cc_start: 0.8033 (mp0) cc_final: 0.7726 (pm20) outliers start: 37 outliers final: 14 residues processed: 159 average time/residue: 1.9773 time to fit residues: 339.1573 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 614 SER 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 1055 SER Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 751 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122450 restraints weight = 13473.807| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.45 r_work: 0.2781 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11917 Z= 0.166 Angle : 0.587 11.201 16272 Z= 0.313 Chirality : 0.041 0.190 1820 Planarity : 0.004 0.056 1873 Dihedral : 15.781 177.865 2119 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.21 % Allowed : 23.31 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1252 helix: 0.84 (0.20), residues: 742 sheet: -1.97 (0.66), residues: 73 loop : -1.78 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 PHE 0.011 0.001 PHE C 51 TYR 0.017 0.001 TYR A1046 ARG 0.008 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 445) hydrogen bonds : angle 3.73164 ( 1274) covalent geometry : bond 0.00378 (11917) covalent geometry : angle 0.58702 (16272) *********************** 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 162 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: A 44 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7721 (tpp80) REVERT: A 149 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: A 383 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7809 (tp) REVERT: A 628 TYR cc_start: 0.8784 (m-80) cc_final: 0.8522 (m-10) REVERT: A 784 PHE cc_start: 0.8661 (m-80) cc_final: 0.8310 (m-80) REVERT: C 144 GLU cc_start: 0.7804 (mp0) cc_final: 0.7539 (mp0) REVERT: C 165 GLU cc_start: 0.8022 (mp0) cc_final: 0.7692 (pm20) REVERT: C 189 ILE cc_start: 0.7649 (mm) cc_final: 0.7439 (mt) outliers start: 38 outliers final: 20 residues processed: 149 average time/residue: 1.3650 time to fit residues: 219.5156 Evaluate side-chains 136 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 149 ARG 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 493 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 581 ASN A 586 GLN A 751 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127132 restraints weight = 13525.270| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.42 r_work: 0.2859 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.6579 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= 0.111 Angle : 0.531 10.179 16272 Z= 0.286 Chirality : 0.039 0.192 1820 Planarity : 0.003 0.054 1873 Dihedral : 15.722 178.291 2119 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.36 % Allowed : 24.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1252 helix: 1.03 (0.20), residues: 737 sheet: -1.69 (0.69), residues: 66 loop : -1.76 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 PHE 0.010 0.001 PHE A 465 TYR 0.015 0.001 TYR A1046 ARG 0.007 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 445) hydrogen bonds : angle 3.56035 ( 1274) covalent geometry : bond 0.00234 (11917) covalent geometry : angle 0.53059 (16272) *********************** 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 157 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: A 44 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7727 (tpp80) REVERT: A 149 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7554 (ttp-170) REVERT: A 383 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 628 TYR cc_start: 0.8727 (m-80) cc_final: 0.8466 (m-10) REVERT: A 781 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8324 (mtmt) REVERT: A 784 PHE cc_start: 0.8682 (m-80) cc_final: 0.8351 (m-80) REVERT: A 849 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8226 (ttpt) REVERT: A 1016 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7588 (ptp-170) REVERT: C 144 GLU cc_start: 0.7846 (mp0) cc_final: 0.7579 (mp0) REVERT: C 162 TYR cc_start: 0.7987 (t80) cc_final: 0.7673 (t80) REVERT: C 165 GLU cc_start: 0.7960 (mp0) cc_final: 0.7645 (mp0) REVERT: C 215 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6870 (pp20) outliers start: 28 outliers final: 15 residues processed: 145 average time/residue: 1.5696 time to fit residues: 244.7201 Evaluate side-chains 135 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 320 ILE 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 614 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 462 ASN A 581 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 = 0.3757 r_free = 0.3757 target = 0.157613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129056 restraints weight = 13435.792| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.46 r_work: 0.2879 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11917 Z= 0.105 Angle : 0.533 9.945 16272 Z= 0.286 Chirality : 0.038 0.194 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.700 179.102 2119 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.03 % Allowed : 24.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1252 helix: 1.22 (0.20), residues: 735 sheet: -1.71 (0.68), residues: 66 loop : -1.65 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 137 HIS 0.002 0.001 HIS A1065 PHE 0.009 0.001 PHE A 465 TYR 0.017 0.001 TYR A1046 ARG 0.007 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 445) hydrogen bonds : angle 3.48053 ( 1274) covalent geometry : bond 0.00217 (11917) covalent geometry : angle 0.53329 (16272) ********************** 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: 24 poor density : 128 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: A 44 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7849 (tpp80) REVERT: A 116 ASP cc_start: 0.7951 (m-30) cc_final: 0.7690 (m-30) REVERT: A 383 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7673 (tp) REVERT: A 628 TYR cc_start: 0.8633 (m-80) cc_final: 0.8366 (m-10) REVERT: A 781 LYS cc_start: 0.8628 (mtmt) cc_final: 0.7858 (mppt) REVERT: A 784 PHE cc_start: 0.8670 (m-80) cc_final: 0.8312 (m-80) REVERT: A 849 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8268 (ttpt) REVERT: A 1016 ARG cc_start: 0.7874 (ptp-170) cc_final: 0.7626 (ptp-170) REVERT: C 41 ARG cc_start: 0.7099 (pmm150) cc_final: 0.6847 (pmt170) REVERT: C 144 GLU cc_start: 0.7762 (mp0) cc_final: 0.7526 (mp0) REVERT: C 162 TYR cc_start: 0.7938 (t80) cc_final: 0.7235 (t80) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 1.3235 time to fit residues: 204.8685 Evaluate side-chains 138 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 320 ILE 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 614 SER Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3751 r_free = 0.3751 target = 0.157194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128461 restraints weight = 13354.270| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.48 r_work: 0.2873 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11917 Z= 0.107 Angle : 0.536 11.382 16272 Z= 0.285 Chirality : 0.039 0.194 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.681 178.828 2119 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.20 % Allowed : 24.83 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1252 helix: 1.28 (0.20), residues: 736 sheet: -1.72 (0.68), residues: 66 loop : -1.66 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 PHE 0.010 0.001 PHE A 169 TYR 0.015 0.001 TYR A1046 ARG 0.007 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 445) hydrogen bonds : angle 3.46301 ( 1274) covalent geometry : bond 0.00226 (11917) covalent geometry : angle 0.53632 (16272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7831.15 seconds wall clock time: 137 minutes 41.74 seconds (8261.74 seconds total)