Starting phenix.real_space_refine on Sun Dec 29 23:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrb_21366/12_2024/6vrb_21366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrb_21366/12_2024/6vrb_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_21366/12_2024/6vrb_21366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrb_21366/12_2024/6vrb_21366.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrb_21366/12_2024/6vrb_21366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrb_21366/12_2024/6vrb_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-5532/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: 7.07, per 1000 atoms: 0.61 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: 2.76 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: 3.95 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: 4.02 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1871 1.32 - 1.44: 3397 1.44 - 1.56: 6486 1.56 - 1.69: 102 1.69 - 1.81: 61 Bond restraints: 11917 Sorted by residual: bond pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" N ILE A 170 " pdb=" CA ILE A 170 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.51e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14894 2.09 - 4.19: 1210 4.19 - 6.28: 119 6.28 - 8.37: 35 8.37 - 10.47: 14 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N GLU A 431 " pdb=" CA GLU A 431 " pdb=" C GLU A 431 " ideal model delta sigma weight residual 114.62 105.17 9.45 1.14e+00 7.69e-01 6.87e+01 angle pdb=" N VAL A 595 " pdb=" CA VAL A 595 " pdb=" C VAL A 595 " ideal model delta sigma weight residual 110.72 104.95 5.77 1.01e+00 9.80e-01 3.27e+01 angle pdb=" N LYS C 65 " pdb=" CA LYS C 65 " pdb=" C LYS C 65 " ideal model delta sigma weight residual 111.02 117.58 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ARG A 316 " pdb=" N ASN A 317 " pdb=" CA ASN A 317 " ideal model delta sigma weight residual 120.28 127.07 -6.79 1.34e+00 5.57e-01 2.57e+01 angle pdb=" C THR A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta sigma weight residual 121.19 128.99 -7.80 1.59e+00 3.96e-01 2.41e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7102 35.54 - 71.09: 206 71.09 - 106.63: 20 106.63 - 142.17: 0 142.17 - 177.71: 4 Dihedral angle restraints: 7332 sinusoidal: 3557 harmonic: 3775 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 232.00 54.29 177.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 37 " pdb=" C1' U B 37 " pdb=" N1 U B 37 " pdb=" C2 U B 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.39 -177.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 51 " pdb=" C1' U B 51 " pdb=" N1 U B 51 " pdb=" C2 U B 51 " ideal model delta sinusoidal sigma weight residual 232.00 58.11 173.89 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1486 0.095 - 0.191: 289 0.191 - 0.286: 43 0.286 - 0.381: 1 0.381 - 0.477: 1 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA LYS C 11 " pdb=" N LYS C 11 " pdb=" C LYS C 11 " pdb=" CB LYS C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN A 532 " pdb=" N ASN A 532 " pdb=" C ASN A 532 " pdb=" CB ASN A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL A 527 " pdb=" CA VAL A 527 " pdb=" CG1 VAL A 527 " pdb=" CG2 VAL A 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1817 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 5 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE C 5 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE C 5 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 508 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN A 508 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN A 508 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 509 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C MET A 594 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 595 " 0.018 2.00e-02 2.50e+03 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 60 2.48 - 3.09: 7248 3.09 - 3.69: 17273 3.69 - 4.30: 26170 4.30 - 4.90: 41661 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG A 212 " pdb=" OG SER A 213 " model vdw 1.877 3.040 nonbonded pdb=" OH TYR C 197 " pdb=" OH TYR C 213 " model vdw 2.166 3.040 nonbonded pdb=" O TYR C 197 " pdb=" O SER C 200 " model vdw 2.178 3.040 nonbonded pdb=" O6 G B 1 " pdb=" O ASN A 309 " model vdw 2.216 3.040 nonbonded pdb=" O2' G B 15 " pdb=" NH1 ARG A 129 " model vdw 2.231 3.120 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- 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= 0.574 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 *********************** 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 : 1.247 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: 1.3856 time to fit residues: 443.0134 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 : 1.282 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11917 Z= 0.188 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 *********************** 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 : 1.243 Fit side-chains REVERT: A 235 SER cc_start: 0.7067 (t) cc_final: 0.6820 (m) REVERT: A 280 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5446 (pm20) REVERT: A 330 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8060 (ptp-170) REVERT: A 383 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7568 (tp) REVERT: A 667 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8320 (mtpt) REVERT: A 818 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 935 ASP cc_start: 0.7896 (m-30) cc_final: 0.7653 (m-30) REVERT: C 17 ASN cc_start: 0.7921 (m-40) cc_final: 0.7669 (m110) REVERT: C 170 ILE cc_start: 0.8738 (tt) cc_final: 0.8520 (mt) outliers start: 59 outliers final: 11 residues processed: 228 average time/residue: 1.4585 time to fit residues: 356.9143 Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 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 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 462 ASN A 714 HIS A 735 GLN A 751 GLN C 142 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11917 Z= 0.157 Angle : 0.556 10.198 16272 Z= 0.302 Chirality : 0.039 0.198 1820 Planarity : 0.004 0.058 1873 Dihedral : 16.002 177.866 2123 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.98 % Allowed : 19.00 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.23), residues: 1252 helix: -0.37 (0.19), residues: 738 sheet: -2.38 (0.67), residues: 70 loop : -1.91 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 137 HIS 0.006 0.001 HIS A 714 PHE 0.010 0.001 PHE C 63 TYR 0.017 0.001 TYR A1046 ARG 0.007 0.001 ARG A 202 *********************** 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 219 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.373 Fit side-chains REVERT: A 235 SER cc_start: 0.6926 (t) cc_final: 0.6684 (m) REVERT: A 383 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7384 (tp) REVERT: A 633 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 667 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8282 (mtpt) REVERT: A 858 ASP cc_start: 0.6950 (t0) cc_final: 0.6470 (t0) REVERT: A 929 MET cc_start: 0.8895 (mmp) cc_final: 0.8686 (mmp) REVERT: C 170 ILE cc_start: 0.8509 (tt) cc_final: 0.8041 (pt) outliers start: 59 outliers final: 17 residues processed: 200 average time/residue: 1.4374 time to fit residues: 309.8453 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 687 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 1074 LEU Chi-restraints excluded: chain C residue 35 GLU 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 116 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11917 Z= 0.267 Angle : 0.657 12.393 16272 Z= 0.350 Chirality : 0.044 0.190 1820 Planarity : 0.004 0.058 1873 Dihedral : 15.983 179.294 2121 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.91 % Allowed : 19.17 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.42 (0.23), residues: 1252 helix: -0.15 (0.19), residues: 744 sheet: -2.50 (0.63), residues: 73 loop : -1.91 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 137 HIS 0.005 0.001 HIS A 670 PHE 0.015 0.002 PHE A 459 TYR 0.013 0.002 TYR A1046 ARG 0.005 0.001 ARG A 202 *********************** 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 224 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 154 time to evaluate : 1.320 Fit side-chains REVERT: A 41 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: A 246 THR cc_start: 0.8823 (p) cc_final: 0.8484 (p) REVERT: A 383 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 513 SER cc_start: 0.9360 (OUTLIER) cc_final: 0.9150 (m) REVERT: A 667 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (mtpt) REVERT: A 735 GLN cc_start: 0.8273 (mt0) cc_final: 0.7956 (mt0) REVERT: A 784 PHE cc_start: 0.8294 (m-80) cc_final: 0.8049 (m-80) REVERT: A 1056 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8957 (tttt) REVERT: C 25 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: C 162 TYR cc_start: 0.7648 (t80) cc_final: 0.7068 (t80) REVERT: C 170 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8105 (pt) REVERT: C 189 ILE cc_start: 0.8009 (mm) cc_final: 0.7764 (mm) outliers start: 70 outliers final: 21 residues processed: 203 average time/residue: 1.3855 time to fit residues: 303.1682 Evaluate side-chains 141 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 101 HIS 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 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1056 LYS Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 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 192 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 586 GLN A 751 GLN A 793 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11917 Z= 0.159 Angle : 0.560 10.857 16272 Z= 0.302 Chirality : 0.040 0.193 1820 Planarity : 0.003 0.056 1873 Dihedral : 15.873 178.301 2121 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.73 % Allowed : 21.71 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.24), residues: 1252 helix: 0.39 (0.20), residues: 741 sheet: -2.39 (0.63), residues: 73 loop : -1.82 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 PHE 0.014 0.001 PHE A 459 TYR 0.011 0.001 TYR A 568 ARG 0.004 0.000 ARG A 202 *********************** 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 186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 1.263 Fit side-chains REVERT: A 179 MET cc_start: 0.8103 (mmm) cc_final: 0.7804 (mmp) REVERT: A 246 THR cc_start: 0.8742 (p) cc_final: 0.8282 (p) REVERT: A 383 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8014 (tp) REVERT: A 466 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7663 (mtmt) REVERT: A 667 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: A 784 PHE cc_start: 0.8460 (m-80) cc_final: 0.8140 (m-80) REVERT: C 170 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8096 (pt) outliers start: 56 outliers final: 15 residues processed: 170 average time/residue: 1.4333 time to fit residues: 262.5564 Evaluate side-chains 131 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE 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 160 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11917 Z= 0.235 Angle : 0.603 11.468 16272 Z= 0.322 Chirality : 0.041 0.187 1820 Planarity : 0.004 0.057 1873 Dihedral : 15.868 177.901 2121 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.14 % Allowed : 22.47 % Favored : 73.40 % 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: -0.74 (0.24), residues: 1252 helix: 0.46 (0.20), residues: 753 sheet: -2.23 (0.65), residues: 73 loop : -1.82 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 137 HIS 0.005 0.001 HIS A 915 PHE 0.011 0.001 PHE C 51 TYR 0.014 0.001 TYR A1046 ARG 0.005 0.001 ARG A 202 *********************** 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 173 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8762 (OUTLIER) cc_final: 0.8486 (t-170) REVERT: A 179 MET cc_start: 0.8256 (mmm) cc_final: 0.8003 (mmp) REVERT: A 246 THR cc_start: 0.8972 (p) cc_final: 0.8637 (p) REVERT: A 383 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8132 (tp) REVERT: A 628 TYR cc_start: 0.8202 (m-80) cc_final: 0.7904 (m-10) REVERT: A 633 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7713 (tp40) REVERT: A 667 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8385 (mtpt) REVERT: A 735 GLN cc_start: 0.8192 (mt0) cc_final: 0.7922 (mt0) REVERT: A 784 PHE cc_start: 0.8595 (m-80) cc_final: 0.8328 (m-80) REVERT: A 1016 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7480 (ptp-170) outliers start: 49 outliers final: 22 residues processed: 160 average time/residue: 1.4135 time to fit residues: 244.0764 Evaluate side-chains 136 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.0570 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.1620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11917 Z= 0.181 Angle : 0.558 10.833 16272 Z= 0.299 Chirality : 0.040 0.189 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.802 177.814 2121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.46 % Allowed : 23.23 % 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: -0.48 (0.24), residues: 1252 helix: 0.72 (0.20), residues: 744 sheet: -2.14 (0.65), residues: 73 loop : -1.76 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 PHE 0.011 0.001 PHE A 459 TYR 0.015 0.001 TYR A1046 ARG 0.004 0.000 ARG A 202 *********************** 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 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8514 (t-170) REVERT: A 246 THR cc_start: 0.8885 (p) cc_final: 0.8593 (p) REVERT: A 383 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 513 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 628 TYR cc_start: 0.8176 (m-80) cc_final: 0.7863 (m-10) REVERT: A 667 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mtpt) REVERT: A 735 GLN cc_start: 0.8158 (mt0) cc_final: 0.7844 (mt0) REVERT: A 784 PHE cc_start: 0.8620 (m-80) cc_final: 0.8343 (m-80) outliers start: 41 outliers final: 20 residues processed: 147 average time/residue: 1.4389 time to fit residues: 228.3274 Evaluate side-chains 131 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 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 170 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11917 Z= 0.167 Angle : 0.548 10.254 16272 Z= 0.293 Chirality : 0.039 0.189 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.698 178.229 2119 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.04 % Allowed : 23.14 % 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: -0.30 (0.24), residues: 1252 helix: 0.90 (0.20), residues: 736 sheet: -2.18 (0.65), residues: 71 loop : -1.70 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 PHE 0.011 0.001 PHE A 459 TYR 0.015 0.001 TYR A1046 ARG 0.004 0.000 ARG A 202 *********************** 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 161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8552 (t-170) REVERT: A 225 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.6803 (mm) REVERT: A 246 THR cc_start: 0.8849 (p) cc_final: 0.8534 (p) REVERT: A 383 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 464 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7840 (p) REVERT: A 513 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8792 (t) REVERT: A 518 TYR cc_start: 0.8524 (m-80) cc_final: 0.8303 (m-80) REVERT: A 667 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8361 (mtpt) REVERT: A 735 GLN cc_start: 0.8143 (mt0) cc_final: 0.7876 (mt0) REVERT: A 784 PHE cc_start: 0.8728 (m-80) cc_final: 0.8441 (m-80) REVERT: C 215 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6550 (pp20) outliers start: 36 outliers final: 20 residues processed: 150 average time/residue: 1.3605 time to fit residues: 220.9877 Evaluate side-chains 138 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 171 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU 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 464 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 832 THR 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 141 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11917 Z= 0.162 Angle : 0.544 10.276 16272 Z= 0.291 Chirality : 0.039 0.192 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.679 178.293 2119 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.36 % Allowed : 24.07 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.24), residues: 1252 helix: 0.96 (0.20), residues: 741 sheet: -1.80 (0.68), residues: 66 loop : -1.69 (0.27), residues: 445 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 0.011 0.001 PHE A 459 TYR 0.012 0.001 TYR A 596 ARG 0.004 0.000 ARG A 202 *********************** 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 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (t-170) REVERT: A 225 LEU cc_start: 0.7740 (tt) cc_final: 0.6815 (mm) REVERT: A 246 THR cc_start: 0.8825 (p) cc_final: 0.8522 (p) REVERT: A 383 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 464 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7883 (p) REVERT: A 513 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8794 (t) REVERT: A 628 TYR cc_start: 0.8139 (m-80) cc_final: 0.7845 (m-10) REVERT: A 667 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8298 (mtpt) REVERT: A 735 GLN cc_start: 0.8132 (mt0) cc_final: 0.7859 (mt0) REVERT: A 784 PHE cc_start: 0.8760 (m-80) cc_final: 0.8512 (m-80) outliers start: 28 outliers final: 17 residues processed: 148 average time/residue: 1.3642 time to fit residues: 219.4164 Evaluate side-chains 138 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11917 Z= 0.168 Angle : 0.544 9.974 16272 Z= 0.290 Chirality : 0.039 0.190 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.692 178.194 2119 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 22.80 % 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: -0.07 (0.24), residues: 1252 helix: 1.07 (0.20), residues: 736 sheet: -1.87 (0.67), residues: 67 loop : -1.62 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 137 HIS 0.004 0.001 HIS A 915 PHE 0.010 0.001 PHE A 459 TYR 0.016 0.001 TYR A1046 ARG 0.004 0.000 ARG A 202 ********************** 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 162 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8536 (t-170) REVERT: A 225 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.6805 (mm) REVERT: A 246 THR cc_start: 0.8851 (p) cc_final: 0.8568 (p) REVERT: A 383 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 464 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7908 (p) REVERT: A 513 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8767 (t) REVERT: A 577 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 667 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8301 (mtpt) REVERT: A 735 GLN cc_start: 0.8139 (mt0) cc_final: 0.7887 (mt0) REVERT: A 784 PHE cc_start: 0.8789 (m-80) cc_final: 0.8527 (m-80) REVERT: C 41 ARG cc_start: 0.7150 (pmt170) cc_final: 0.6603 (pmm150) outliers start: 36 outliers final: 22 residues processed: 149 average time/residue: 1.3180 time to fit residues: 213.0272 Evaluate side-chains 149 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 171 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU 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 464 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 883 SER 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 141 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 0.0000 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.157143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128684 restraints weight = 13344.792| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.37 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11917 Z= 0.152 Angle : 0.541 11.318 16272 Z= 0.288 Chirality : 0.039 0.195 1820 Planarity : 0.003 0.055 1873 Dihedral : 15.664 178.517 2119 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.79 % Allowed : 23.65 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.24), residues: 1252 helix: 1.14 (0.20), residues: 741 sheet: -1.72 (0.67), residues: 66 loop : -1.64 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 137 HIS 0.003 0.001 HIS A 915 PHE 0.023 0.001 PHE A 169 TYR 0.025 0.001 TYR C 162 ARG 0.004 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.42 seconds wall clock time: 79 minutes 52.18 seconds (4792.18 seconds total)