Starting phenix.real_space_refine on Thu Sep 18 07:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvy_43572/09_2025/8vvy_43572.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.177 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 9476 2.51 5 N 2607 2.21 5 O 2788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14950 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5923 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 13, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 9027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9027 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 70, 'TRANS': 1105} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.23 Number of scatterers: 14950 At special positions: 0 Unit cell: (103.55, 128.25, 161.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2788 8.00 N 2607 7.00 C 9476 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: 1.27 Conformation dependent library (CDL) restraints added in 691.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 3 sheets defined 78.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 removed outlier: 4.111A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 removed outlier: 4.359A pdb=" N TYR A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 79 through 103 removed outlier: 3.528A pdb=" N PHE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.918A pdb=" N ASP A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 removed outlier: 4.990A pdb=" N GLY A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 122 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 136 through 158 removed outlier: 5.005A pdb=" N LYS A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLN A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 176 removed outlier: 4.417A pdb=" N ILE A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.736A pdb=" N GLN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 removed outlier: 3.544A pdb=" N TYR A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.735A pdb=" N GLU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 298 through 321 removed outlier: 3.915A pdb=" N CYS A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.536A pdb=" N ASN A 326 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.710A pdb=" N TYR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 371 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.624A pdb=" N HIS A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 462 Processing helix chain 'A' and resid 463 through 492 removed outlier: 4.472A pdb=" N LYS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 469 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.597A pdb=" N TYR A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 653 through 688 removed outlier: 5.355A pdb=" N ARG A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 removed outlier: 3.808A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'C' and resid 14 through 24 removed outlier: 3.813A pdb=" N HIS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 30 through 42 removed outlier: 4.114A pdb=" N PHE C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.546A pdb=" N ASN C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 Proline residue: C 85 - end of helix Processing helix chain 'C' and resid 91 through 107 removed outlier: 4.285A pdb=" N THR C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.871A pdb=" N ILE C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 155 Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.974A pdb=" N GLU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.856A pdb=" N HIS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 214 removed outlier: 3.793A pdb=" N ARG C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.784A pdb=" N ASP C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 260 removed outlier: 3.932A pdb=" N ILE C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 279 removed outlier: 4.201A pdb=" N ASP C 268 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 282 through 300 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.538A pdb=" N VAL C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 377 removed outlier: 3.547A pdb=" N VAL C 362 " --> pdb=" O MET C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 388 Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 401 through 419 Processing helix chain 'C' and resid 432 through 453 Proline residue: C 446 - end of helix Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 460 through 478 removed outlier: 3.694A pdb=" N ARG C 464 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 485 through 498 removed outlier: 3.869A pdb=" N SER C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 521 removed outlier: 4.473A pdb=" N ARG C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 527 removed outlier: 3.592A pdb=" N ALA C 525 " --> pdb=" O PRO C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 542 Proline residue: C 535 - end of helix removed outlier: 3.779A pdb=" N ALA C 542 " --> pdb=" O MET C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 3.734A pdb=" N TRP C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 590 removed outlier: 4.484A pdb=" N GLY C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU C 580 " --> pdb=" O PRO C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 618 removed outlier: 7.065A pdb=" N ASP C 615 " --> pdb=" O GLY C 611 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG C 616 " --> pdb=" O HIS C 612 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY C 618 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.583A pdb=" N LEU C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 651 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 660 through 674 removed outlier: 3.871A pdb=" N ARG C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 695 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.613A pdb=" N VAL C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 713 Processing helix chain 'C' and resid 719 through 736 Processing helix chain 'C' and resid 737 through 741 removed outlier: 3.915A pdb=" N VAL C 741 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 removed outlier: 3.975A pdb=" N SER C 757 " --> pdb=" O ARG C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 Processing helix chain 'C' and resid 787 through 799 Proline residue: C 795 - end of helix Processing helix chain 'C' and resid 808 through 826 removed outlier: 4.404A pdb=" N CYS C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 842 removed outlier: 4.119A pdb=" N SER C 835 " --> pdb=" O ALA C 831 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 865 removed outlier: 4.200A pdb=" N ALA C 865 " --> pdb=" O VAL C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 882 removed outlier: 3.908A pdb=" N VAL C 876 " --> pdb=" O GLU C 872 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 903 removed outlier: 3.639A pdb=" N ALA C 901 " --> pdb=" O GLY C 897 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 918 Proline residue: C 909 - end of helix Processing helix chain 'C' and resid 921 through 936 Processing helix chain 'C' and resid 937 through 940 Processing helix chain 'C' and resid 941 through 953 removed outlier: 4.765A pdb=" N GLU C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP C 947 " --> pdb=" O PRO C 943 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 948 " --> pdb=" O TYR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 976 removed outlier: 3.769A pdb=" N LEU C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 992 Proline residue: C 984 - end of helix Processing helix chain 'C' and resid 994 through 1008 removed outlier: 3.747A pdb=" N THR C1000 " --> pdb=" O HIS C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1029 removed outlier: 5.341A pdb=" N GLY C1025 " --> pdb=" O LYS C1021 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU C1026 " --> pdb=" O SER C1022 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C1027 " --> pdb=" O PHE C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1053 Processing helix chain 'C' and resid 1054 through 1059 removed outlier: 4.640A pdb=" N ASP C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1063 Processing helix chain 'C' and resid 1064 through 1073 removed outlier: 3.685A pdb=" N GLU C1071 " --> pdb=" O LEU C1067 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C1072 " --> pdb=" O LEU C1068 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1073 " --> pdb=" O TYR C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1112 removed outlier: 3.658A pdb=" N ARG C1098 " --> pdb=" O GLY C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1116 removed outlier: 3.605A pdb=" N LEU C1116 " --> pdb=" O LEU C1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1113 through 1116' Processing helix chain 'C' and resid 1117 through 1130 removed outlier: 4.228A pdb=" N LYS C1130 " --> pdb=" O GLU C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1150 removed outlier: 3.853A pdb=" N THR C1148 " --> pdb=" O ALA C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1171 removed outlier: 4.640A pdb=" N ASP C1159 " --> pdb=" O LEU C1155 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG C1160 " --> pdb=" O GLN C1156 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU C1163 " --> pdb=" O ASP C1159 " (cutoff:3.500A) Proline residue: C1164 - end of helix Processing helix chain 'C' and resid 1178 through 1201 Processing helix chain 'C' and resid 1203 through 1207 Processing helix chain 'C' and resid 1208 through 1220 removed outlier: 3.633A pdb=" N ALA C1212 " --> pdb=" O SER C1208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.659A pdb=" N THR A 557 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR A 564 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR A 565 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 586 Processing sheet with id=AA3, first strand: chain 'C' and resid 1079 through 1080 removed outlier: 4.436A pdb=" N ARG C1080 " --> pdb=" O VAL C1091 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C1091 " --> pdb=" O ARG C1080 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 972 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4823 1.34 - 1.46: 1591 1.46 - 1.57: 8670 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 15204 Sorted by residual: bond pdb=" N ARG C 779 " pdb=" CA ARG C 779 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.22e+01 bond pdb=" N VAL C 783 " pdb=" CA VAL C 783 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.61e+00 bond pdb=" C ARG C 779 " pdb=" O ARG C 779 " ideal model delta sigma weight residual 1.233 1.247 -0.014 4.80e-03 4.34e+04 8.63e+00 bond pdb=" N ILE C 789 " pdb=" CA ILE C 789 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.42e+00 bond pdb=" N TYR C 785 " pdb=" CA TYR C 785 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.06e+00 ... (remaining 15199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20233 2.05 - 4.10: 273 4.10 - 6.16: 54 6.16 - 8.21: 7 8.21 - 10.26: 4 Bond angle restraints: 20571 Sorted by residual: angle pdb=" N ILE A 649 " pdb=" CA ILE A 649 " pdb=" C ILE A 649 " ideal model delta sigma weight residual 113.71 109.27 4.44 9.50e-01 1.11e+00 2.19e+01 angle pdb=" N THR C 219 " pdb=" CA THR C 219 " pdb=" C THR C 219 " ideal model delta sigma weight residual 114.56 109.97 4.59 1.27e+00 6.20e-01 1.31e+01 angle pdb=" C LYS A 688 " pdb=" CA LYS A 688 " pdb=" CB LYS A 688 " ideal model delta sigma weight residual 116.34 111.37 4.97 1.40e+00 5.10e-01 1.26e+01 angle pdb=" N GLU C 969 " pdb=" CA GLU C 969 " pdb=" CB GLU C 969 " ideal model delta sigma weight residual 110.28 115.43 -5.15 1.55e+00 4.16e-01 1.10e+01 angle pdb=" CA ASP C 784 " pdb=" C ASP C 784 " pdb=" O ASP C 784 " ideal model delta sigma weight residual 122.31 118.07 4.24 1.31e+00 5.83e-01 1.05e+01 ... (remaining 20566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 8327 17.43 - 34.85: 889 34.85 - 52.28: 141 52.28 - 69.71: 33 69.71 - 87.13: 18 Dihedral angle restraints: 9408 sinusoidal: 3831 harmonic: 5577 Sorted by residual: dihedral pdb=" CA LEU C 67 " pdb=" C LEU C 67 " pdb=" N LEU C 68 " pdb=" CA LEU C 68 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU C 64 " pdb=" C LEU C 64 " pdb=" N LEU C 65 " pdb=" CA LEU C 65 " ideal model delta harmonic sigma weight residual 180.00 159.58 20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA THR A 248 " pdb=" C THR A 248 " pdb=" N GLN A 249 " pdb=" CA GLN A 249 " ideal model delta harmonic sigma weight residual -180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 9405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1591 0.034 - 0.067: 575 0.067 - 0.101: 179 0.101 - 0.135: 42 0.135 - 0.169: 7 Chirality restraints: 2394 Sorted by residual: chirality pdb=" CA ILE C 789 " pdb=" N ILE C 789 " pdb=" C ILE C 789 " pdb=" CB ILE C 789 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CB ILE C1016 " pdb=" CA ILE C1016 " pdb=" CG1 ILE C1016 " pdb=" CG2 ILE C1016 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA VAL C 783 " pdb=" N VAL C 783 " pdb=" C VAL C 783 " pdb=" CB VAL C 783 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2391 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 675 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.35e+00 pdb=" C LEU A 675 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 675 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 676 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C1208 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C1209 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C1209 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C1209 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 85 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C THR A 85 " 0.028 2.00e-02 2.50e+03 pdb=" O THR A 85 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 86 " -0.009 2.00e-02 2.50e+03 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2905 2.77 - 3.31: 15083 3.31 - 3.84: 23750 3.84 - 4.37: 26187 4.37 - 4.90: 45710 Nonbonded interactions: 113635 Sorted by model distance: nonbonded pdb=" O GLY A 177 " pdb=" OG1 THR A 189 " model vdw 2.243 3.040 nonbonded pdb=" O ALA C1198 " pdb=" OG1 THR C1201 " model vdw 2.247 3.040 nonbonded pdb=" O SER A 551 " pdb=" OG1 THR A 570 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 225 " pdb=" O LEU A 260 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU A 235 " pdb=" NH2 ARG A 239 " model vdw 2.258 3.120 ... (remaining 113630 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: 1.210 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.003 0.053 15204 Z= 0.164 Angle : 0.611 10.261 20571 Z= 0.317 Chirality : 0.039 0.169 2394 Planarity : 0.004 0.046 2652 Dihedral : 14.712 87.131 5774 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 0.18 % Allowed : 0.49 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.20), residues: 1892 helix: 1.24 (0.15), residues: 1294 sheet: 2.23 (1.70), residues: 10 loop : -1.05 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.020 0.001 TYR C1133 PHE 0.024 0.001 PHE C 855 TRP 0.005 0.001 TRP A 10 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00319 (15204) covalent geometry : angle 0.61150 (20571) hydrogen bonds : bond 0.13358 ( 972) hydrogen bonds : angle 5.48329 ( 2859) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8669 (mt) cc_final: 0.8398 (mt) REVERT: A 91 TYR cc_start: 0.8236 (t80) cc_final: 0.8017 (t80) REVERT: A 133 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7685 (tmm160) REVERT: A 719 ASP cc_start: 0.8205 (m-30) cc_final: 0.7890 (m-30) REVERT: C 789 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7054 (pt) REVERT: C 1084 MET cc_start: 0.6224 (tpt) cc_final: 0.6015 (tpp) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.1260 time to fit residues: 30.5911 Evaluate side-chains 131 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 789 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 608 HIS C 927 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.210897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142705 restraints weight = 20881.318| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.59 r_work: 0.3415 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15204 Z= 0.175 Angle : 0.621 10.457 20571 Z= 0.311 Chirality : 0.041 0.151 2394 Planarity : 0.004 0.047 2652 Dihedral : 4.398 58.882 2061 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.09 % Allowed : 6.86 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.20), residues: 1892 helix: 1.45 (0.15), residues: 1306 sheet: 2.78 (1.88), residues: 10 loop : -0.84 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.022 0.002 TYR A 528 PHE 0.020 0.001 PHE A 367 TRP 0.009 0.001 TRP A 132 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00421 (15204) covalent geometry : angle 0.62148 (20571) hydrogen bonds : bond 0.04945 ( 972) hydrogen bonds : angle 4.37521 ( 2859) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7760 (mmm) cc_final: 0.7499 (mmm) REVERT: A 91 TYR cc_start: 0.8316 (t80) cc_final: 0.8092 (t80) REVERT: A 133 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7906 (tmm-80) REVERT: A 171 GLN cc_start: 0.8419 (tm130) cc_final: 0.8072 (tm-30) REVERT: A 176 LEU cc_start: 0.9297 (mp) cc_final: 0.9034 (mp) REVERT: A 719 ASP cc_start: 0.8358 (m-30) cc_final: 0.8070 (m-30) REVERT: C 42 MET cc_start: 0.7148 (tpp) cc_final: 0.6501 (tpt) REVERT: C 855 PHE cc_start: 0.8389 (m-80) cc_final: 0.7498 (m-80) REVERT: C 954 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 1084 MET cc_start: 0.6573 (tpt) cc_final: 0.6348 (tpp) outliers start: 18 outliers final: 10 residues processed: 145 average time/residue: 0.1157 time to fit residues: 25.8183 Evaluate side-chains 137 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 139 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 144 optimal weight: 0.8980 chunk 63 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 188 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.215201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146123 restraints weight = 20886.850| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.81 r_work: 0.3494 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15204 Z= 0.109 Angle : 0.541 9.057 20571 Z= 0.270 Chirality : 0.037 0.155 2394 Planarity : 0.004 0.042 2652 Dihedral : 4.205 58.246 2059 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.85 % Allowed : 8.74 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.20), residues: 1892 helix: 1.69 (0.15), residues: 1307 sheet: 3.31 (1.90), residues: 10 loop : -0.77 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.016 0.001 TYR A 528 PHE 0.017 0.001 PHE A 534 TRP 0.009 0.001 TRP A 132 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00221 (15204) covalent geometry : angle 0.54144 (20571) hydrogen bonds : bond 0.03714 ( 972) hydrogen bonds : angle 4.06657 ( 2859) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7631 (mmm) cc_final: 0.7383 (mmm) REVERT: A 91 TYR cc_start: 0.8315 (t80) cc_final: 0.8068 (t80) REVERT: A 171 GLN cc_start: 0.8338 (tm130) cc_final: 0.7845 (tm-30) REVERT: A 719 ASP cc_start: 0.8313 (m-30) cc_final: 0.8030 (m-30) REVERT: C 42 MET cc_start: 0.7089 (tpp) cc_final: 0.6648 (tpt) REVERT: C 277 PHE cc_start: 0.7299 (m-80) cc_final: 0.7096 (m-80) REVERT: C 558 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 855 PHE cc_start: 0.8318 (m-80) cc_final: 0.7356 (m-80) REVERT: C 1084 MET cc_start: 0.6576 (tpt) cc_final: 0.6320 (tpp) REVERT: C 1088 LYS cc_start: 0.6122 (tptm) cc_final: 0.5672 (tppt) outliers start: 14 outliers final: 9 residues processed: 159 average time/residue: 0.1241 time to fit residues: 30.0726 Evaluate side-chains 138 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 944 TYR Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 0.0040 chunk 10 optimal weight: 9.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.209393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146934 restraints weight = 21456.341| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.36 r_work: 0.3439 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15204 Z= 0.201 Angle : 0.619 10.858 20571 Z= 0.308 Chirality : 0.041 0.162 2394 Planarity : 0.004 0.050 2652 Dihedral : 4.322 53.424 2059 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.03 % Allowed : 11.90 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.20), residues: 1892 helix: 1.48 (0.15), residues: 1321 sheet: 3.64 (1.94), residues: 10 loop : -0.95 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.016 0.002 TYR A 342 PHE 0.024 0.002 PHE A 367 TRP 0.009 0.001 TRP A 132 HIS 0.006 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00502 (15204) covalent geometry : angle 0.61909 (20571) hydrogen bonds : bond 0.04983 ( 972) hydrogen bonds : angle 4.24319 ( 2859) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.7611 (mmm) cc_final: 0.7311 (mmm) REVERT: A 91 TYR cc_start: 0.8474 (t80) cc_final: 0.8203 (t80) REVERT: A 672 ARG cc_start: 0.7088 (tpp80) cc_final: 0.6628 (tpt-90) REVERT: A 717 CYS cc_start: 0.8806 (m) cc_final: 0.8401 (m) REVERT: A 719 ASP cc_start: 0.8376 (m-30) cc_final: 0.8103 (m-30) REVERT: C 42 MET cc_start: 0.7317 (tpp) cc_final: 0.6768 (tpt) REVERT: C 558 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8011 (mm-30) REVERT: C 684 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 855 PHE cc_start: 0.8615 (m-80) cc_final: 0.7854 (m-80) REVERT: C 1084 MET cc_start: 0.6348 (tpt) cc_final: 0.6101 (tpp) REVERT: C 1088 LYS cc_start: 0.5899 (tptm) cc_final: 0.5540 (tppt) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.1204 time to fit residues: 26.5407 Evaluate side-chains 145 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 944 TYR Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 153 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146571 restraints weight = 20961.006| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.57 r_work: 0.3456 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15204 Z= 0.110 Angle : 0.535 10.232 20571 Z= 0.268 Chirality : 0.037 0.155 2394 Planarity : 0.004 0.041 2652 Dihedral : 4.172 54.772 2059 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.21 % Allowed : 12.87 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.20), residues: 1892 helix: 1.71 (0.15), residues: 1328 sheet: 3.70 (1.93), residues: 10 loop : -0.89 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.014 0.001 TYR A 342 PHE 0.014 0.001 PHE C 277 TRP 0.010 0.001 TRP A 132 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00230 (15204) covalent geometry : angle 0.53547 (20571) hydrogen bonds : bond 0.03707 ( 972) hydrogen bonds : angle 3.97684 ( 2859) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7689 (mmm) cc_final: 0.7385 (mmm) REVERT: A 91 TYR cc_start: 0.8366 (t80) cc_final: 0.8016 (t80) REVERT: A 672 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6545 (tpt-90) REVERT: A 719 ASP cc_start: 0.8339 (m-30) cc_final: 0.8064 (m-30) REVERT: A 720 ILE cc_start: 0.8566 (mt) cc_final: 0.8331 (mt) REVERT: C 42 MET cc_start: 0.7221 (tpp) cc_final: 0.6870 (tpt) REVERT: C 277 PHE cc_start: 0.7363 (m-80) cc_final: 0.7138 (m-80) REVERT: C 558 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 684 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8404 (mm) REVERT: C 851 LYS cc_start: 0.8095 (tptp) cc_final: 0.7595 (tptp) REVERT: C 855 PHE cc_start: 0.8312 (m-80) cc_final: 0.7523 (m-80) REVERT: C 1084 MET cc_start: 0.6374 (tpt) cc_final: 0.6139 (tpp) REVERT: C 1088 LYS cc_start: 0.5967 (tptm) cc_final: 0.5616 (tppt) outliers start: 20 outliers final: 14 residues processed: 154 average time/residue: 0.1120 time to fit residues: 27.0241 Evaluate side-chains 145 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 944 TYR Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.212051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142674 restraints weight = 20741.101| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.63 r_work: 0.3418 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15204 Z= 0.144 Angle : 0.559 9.331 20571 Z= 0.281 Chirality : 0.039 0.166 2394 Planarity : 0.004 0.042 2652 Dihedral : 4.186 53.473 2059 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.52 % Allowed : 13.48 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1892 helix: 1.69 (0.15), residues: 1322 sheet: 3.71 (1.94), residues: 10 loop : -0.94 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.017 0.001 TYR C1133 PHE 0.022 0.001 PHE C 222 TRP 0.016 0.001 TRP C 949 HIS 0.006 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00345 (15204) covalent geometry : angle 0.55871 (20571) hydrogen bonds : bond 0.04198 ( 972) hydrogen bonds : angle 4.07827 ( 2859) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7695 (mmm) cc_final: 0.7378 (mmm) REVERT: A 91 TYR cc_start: 0.8385 (t80) cc_final: 0.8046 (t80) REVERT: A 175 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 672 ARG cc_start: 0.6983 (tpp80) cc_final: 0.6600 (tpt-90) REVERT: A 717 CYS cc_start: 0.8502 (m) cc_final: 0.8162 (m) REVERT: A 719 ASP cc_start: 0.8384 (m-30) cc_final: 0.8120 (m-30) REVERT: C 42 MET cc_start: 0.7216 (tpp) cc_final: 0.6843 (tpt) REVERT: C 143 ARG cc_start: 0.6862 (mmp-170) cc_final: 0.6638 (mmm160) REVERT: C 183 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: C 558 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 684 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 851 LYS cc_start: 0.8134 (tptp) cc_final: 0.7669 (tptp) REVERT: C 855 PHE cc_start: 0.8352 (m-80) cc_final: 0.7646 (m-80) REVERT: C 954 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: C 1084 MET cc_start: 0.6370 (tpt) cc_final: 0.6137 (tpp) REVERT: C 1088 LYS cc_start: 0.6028 (tptm) cc_final: 0.5658 (tppt) outliers start: 25 outliers final: 19 residues processed: 151 average time/residue: 0.1154 time to fit residues: 26.8651 Evaluate side-chains 150 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.213564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144338 restraints weight = 20809.913| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.69 r_work: 0.3462 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15204 Z= 0.114 Angle : 0.544 10.788 20571 Z= 0.272 Chirality : 0.037 0.154 2394 Planarity : 0.004 0.041 2652 Dihedral : 4.120 53.829 2059 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.58 % Allowed : 14.21 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1892 helix: 1.77 (0.15), residues: 1324 sheet: 3.77 (1.95), residues: 10 loop : -0.86 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.013 0.001 TYR A 342 PHE 0.014 0.001 PHE A 367 TRP 0.013 0.001 TRP C 949 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00251 (15204) covalent geometry : angle 0.54373 (20571) hydrogen bonds : bond 0.03729 ( 972) hydrogen bonds : angle 3.98876 ( 2859) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7626 (mmm) cc_final: 0.7311 (mmm) REVERT: A 91 TYR cc_start: 0.8380 (t80) cc_final: 0.8048 (t80) REVERT: A 175 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 672 ARG cc_start: 0.6939 (tpp80) cc_final: 0.6507 (tpt-90) REVERT: A 719 ASP cc_start: 0.8388 (m-30) cc_final: 0.8095 (m-30) REVERT: C 42 MET cc_start: 0.7172 (tpp) cc_final: 0.6907 (tpt) REVERT: C 183 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: C 277 PHE cc_start: 0.7423 (m-80) cc_final: 0.7202 (m-80) REVERT: C 558 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 684 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8458 (mm) REVERT: C 851 LYS cc_start: 0.8145 (tptp) cc_final: 0.7684 (tptp) REVERT: C 855 PHE cc_start: 0.8368 (m-80) cc_final: 0.7672 (m-80) REVERT: C 954 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: C 1084 MET cc_start: 0.6226 (tpt) cc_final: 0.5986 (tpp) REVERT: C 1088 LYS cc_start: 0.6021 (tptm) cc_final: 0.5696 (tppt) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.1127 time to fit residues: 26.4848 Evaluate side-chains 147 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 144 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.211340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141457 restraints weight = 20836.747| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.71 r_work: 0.3400 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15204 Z= 0.151 Angle : 0.592 13.053 20571 Z= 0.292 Chirality : 0.039 0.180 2394 Planarity : 0.004 0.041 2652 Dihedral : 4.181 52.157 2059 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.64 % Allowed : 14.27 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1892 helix: 1.67 (0.15), residues: 1323 sheet: 3.83 (1.97), residues: 10 loop : -0.86 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.019 0.002 TYR A 528 PHE 0.019 0.001 PHE A 367 TRP 0.011 0.001 TRP C 949 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00364 (15204) covalent geometry : angle 0.59246 (20571) hydrogen bonds : bond 0.04319 ( 972) hydrogen bonds : angle 4.11306 ( 2859) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7650 (mmm) cc_final: 0.7328 (mmm) REVERT: A 91 TYR cc_start: 0.8421 (t80) cc_final: 0.8088 (t80) REVERT: A 175 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 719 ASP cc_start: 0.8413 (m-30) cc_final: 0.8119 (m-30) REVERT: C 42 MET cc_start: 0.7303 (tpp) cc_final: 0.7078 (tpt) REVERT: C 183 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: C 558 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 684 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8469 (mm) REVERT: C 855 PHE cc_start: 0.8406 (m-80) cc_final: 0.7719 (m-80) REVERT: C 954 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: C 1069 TYR cc_start: 0.7884 (m-10) cc_final: 0.7580 (m-80) REVERT: C 1084 MET cc_start: 0.6118 (tpt) cc_final: 0.5829 (tpp) REVERT: C 1132 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6198 (t70) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.1173 time to fit residues: 27.3795 Evaluate side-chains 154 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 606 GLN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1132 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.212860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156316 restraints weight = 20966.428| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.76 r_work: 0.3467 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15204 Z= 0.124 Angle : 0.569 13.840 20571 Z= 0.280 Chirality : 0.038 0.154 2394 Planarity : 0.004 0.043 2652 Dihedral : 4.129 52.350 2059 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.52 % Allowed : 14.45 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.20), residues: 1892 helix: 1.76 (0.15), residues: 1324 sheet: 3.89 (1.99), residues: 10 loop : -0.81 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.014 0.001 TYR A 342 PHE 0.015 0.001 PHE A 367 TRP 0.012 0.001 TRP C 949 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00286 (15204) covalent geometry : angle 0.56907 (20571) hydrogen bonds : bond 0.03879 ( 972) hydrogen bonds : angle 4.02113 ( 2859) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7591 (mmm) cc_final: 0.7267 (mmm) REVERT: A 91 TYR cc_start: 0.8503 (t80) cc_final: 0.8170 (t80) REVERT: A 175 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 672 ARG cc_start: 0.7057 (tpp80) cc_final: 0.6624 (tpt-90) REVERT: C 26 MET cc_start: 0.7308 (mpp) cc_final: 0.6971 (mpp) REVERT: C 183 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: C 558 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7841 (mm-30) REVERT: C 684 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 855 PHE cc_start: 0.8543 (m-80) cc_final: 0.7861 (m-80) REVERT: C 954 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: C 1069 TYR cc_start: 0.7886 (m-10) cc_final: 0.7628 (m-80) REVERT: C 1084 MET cc_start: 0.5811 (tpt) cc_final: 0.5538 (tpp) REVERT: C 1132 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6118 (t70) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.1247 time to fit residues: 28.2980 Evaluate side-chains 149 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 606 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1132 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 145 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 112 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.214240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145299 restraints weight = 20933.896| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.53 r_work: 0.3485 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15204 Z= 0.105 Angle : 0.554 15.300 20571 Z= 0.270 Chirality : 0.037 0.153 2394 Planarity : 0.004 0.046 2652 Dihedral : 4.018 53.437 2059 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.21 % Allowed : 14.81 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.20), residues: 1892 helix: 1.88 (0.15), residues: 1325 sheet: 3.84 (1.99), residues: 10 loop : -0.83 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.026 0.001 TYR C1133 PHE 0.013 0.001 PHE C 953 TRP 0.013 0.001 TRP C 949 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00220 (15204) covalent geometry : angle 0.55363 (20571) hydrogen bonds : bond 0.03320 ( 972) hydrogen bonds : angle 3.91692 ( 2859) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7641 (mmm) cc_final: 0.7316 (mmm) REVERT: A 175 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 672 ARG cc_start: 0.6953 (tpp80) cc_final: 0.6560 (tpt-90) REVERT: C 558 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 606 MET cc_start: 0.8966 (tpt) cc_final: 0.8505 (tpt) REVERT: C 684 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8391 (mm) REVERT: C 851 LYS cc_start: 0.8020 (tptp) cc_final: 0.7488 (mmmt) REVERT: C 855 PHE cc_start: 0.8289 (m-80) cc_final: 0.7627 (m-80) REVERT: C 954 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: C 1084 MET cc_start: 0.6198 (tpt) cc_final: 0.5884 (tpp) REVERT: C 1132 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.5960 (t70) outliers start: 20 outliers final: 15 residues processed: 150 average time/residue: 0.1293 time to fit residues: 29.1625 Evaluate side-chains 141 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 606 GLN Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1132 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 39 optimal weight: 0.0040 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 164 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.214028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145002 restraints weight = 20865.535| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.65 r_work: 0.3496 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15204 Z= 0.109 Angle : 0.562 14.250 20571 Z= 0.275 Chirality : 0.037 0.153 2394 Planarity : 0.004 0.044 2652 Dihedral : 3.988 53.378 2059 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 1.40 % Allowed : 14.63 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.20), residues: 1892 helix: 1.90 (0.15), residues: 1326 sheet: 3.87 (1.96), residues: 10 loop : -0.75 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 107 TYR 0.025 0.001 TYR C1133 PHE 0.025 0.001 PHE C1023 TRP 0.011 0.001 TRP C 949 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00236 (15204) covalent geometry : angle 0.56198 (20571) hydrogen bonds : bond 0.03386 ( 972) hydrogen bonds : angle 3.91032 ( 2859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4207.80 seconds wall clock time: 72 minutes 42.24 seconds (4362.24 seconds total)