Starting phenix.real_space_refine on Thu Feb 5 16:00:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l4l_62815/02_2026/9l4l_62815.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 146 5.16 5 C 11551 2.51 5 N 3167 2.21 5 O 3322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6989 Classifications: {'peptide': 889} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7661 Classifications: {'peptide': 975} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 35, 'TRANS': 939} Chain breaks: 7 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 780 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "C" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2756 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.87, per 1000 atoms: 0.21 Number of scatterers: 18186 At special positions: 0 Unit cell: (109.65, 131.75, 192.1, 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 146 16.00 O 3322 8.00 N 3167 7.00 C 11551 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: 1.68 Conformation dependent library (CDL) restraints added in 875.2 milliseconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 18 sheets defined 51.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 157 through 172 removed outlier: 4.472A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 247 through 253 removed outlier: 4.078A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.653A pdb=" N ASP A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.109A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 397 through 415 Processing helix chain 'A' and resid 417 through 424 removed outlier: 4.418A pdb=" N THR A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.568A pdb=" N PHE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 460 removed outlier: 4.521A pdb=" N ALA A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 493 through 496 removed outlier: 3.610A pdb=" N LYS A 496 " --> pdb=" O ARG A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 520 through 526 removed outlier: 4.038A pdb=" N ASP A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 548 through 561 removed outlier: 4.427A pdb=" N GLN A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 Processing helix chain 'A' and resid 578 through 589 removed outlier: 4.269A pdb=" N LYS A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 586 " --> pdb=" O LYS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'A' and resid 614 through 623 Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.510A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 removed outlier: 3.665A pdb=" N ASP A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS A 683 " --> pdb=" O GLN A 679 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 740 through 751 removed outlier: 3.726A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 780 removed outlier: 3.872A pdb=" N ALA A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 810 Processing helix chain 'A' and resid 824 through 836 Processing helix chain 'A' and resid 853 through 867 Processing helix chain 'A' and resid 881 through 893 removed outlier: 3.628A pdb=" N VAL A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 923 removed outlier: 4.034A pdb=" N GLU A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 950 Processing helix chain 'A' and resid 967 through 981 removed outlier: 4.117A pdb=" N ASP A 973 " --> pdb=" O PHE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1009 removed outlier: 3.927A pdb=" N LYS A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1038 Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'D' and resid 59 through 70 removed outlier: 3.790A pdb=" N GLY D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 136 through 150 Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.575A pdb=" N ARG D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 268 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 321 through 327 removed outlier: 3.556A pdb=" N LYS D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.556A pdb=" N TRP D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.798A pdb=" N LEU D 367 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 497 through 511 removed outlier: 3.598A pdb=" N LEU D 501 " --> pdb=" O THR D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 Processing helix chain 'D' and resid 547 through 555 Processing helix chain 'D' and resid 557 through 565 Processing helix chain 'D' and resid 585 through 598 Processing helix chain 'D' and resid 618 through 625 removed outlier: 4.038A pdb=" N LYS D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 4.205A pdb=" N MET D 633 " --> pdb=" O HIS D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 removed outlier: 4.084A pdb=" N LEU D 649 " --> pdb=" O VAL D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 674 Processing helix chain 'D' and resid 680 through 695 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 716 through 727 Processing helix chain 'D' and resid 756 through 756 No H-bonds generated for 'chain 'D' and resid 756 through 756' Processing helix chain 'D' and resid 759 through 762 No H-bonds generated for 'chain 'D' and resid 759 through 762' Processing helix chain 'D' and resid 764 through 780 Processing helix chain 'D' and resid 794 through 807 removed outlier: 4.417A pdb=" N HIS D 807 " --> pdb=" O ALA D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 828 removed outlier: 3.736A pdb=" N VAL D 826 " --> pdb=" O THR D 823 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN D 827 " --> pdb=" O PRO D 824 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS D 828 " --> pdb=" O GLY D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 836 removed outlier: 3.811A pdb=" N VAL D 833 " --> pdb=" O LEU D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 863 removed outlier: 3.548A pdb=" N HIS D 863 " --> pdb=" O GLU D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 893 Processing helix chain 'D' and resid 907 through 920 Proline residue: D 913 - end of helix removed outlier: 3.666A pdb=" N VAL D 920 " --> pdb=" O ASP D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 950 Processing helix chain 'D' and resid 963 through 976 removed outlier: 3.754A pdb=" N GLY D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1005 removed outlier: 3.524A pdb=" N MET D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1050 through 1064 Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.539A pdb=" N GLY D1081 " --> pdb=" O LEU D1077 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D1082 " --> pdb=" O GLY D1078 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN D1091 " --> pdb=" O GLU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1121 Processing helix chain 'D' and resid 1135 through 1147 Processing helix chain 'D' and resid 1159 through 1163 Processing helix chain 'D' and resid 1164 through 1177 Processing helix chain 'D' and resid 1192 through 1200 removed outlier: 4.450A pdb=" N TYR D1196 " --> pdb=" O GLU D1192 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS D1199 " --> pdb=" O ARG D1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.523A pdb=" N GLU B 45 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 47 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 99 through 124 Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.935A pdb=" N THR C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.200A pdb=" N GLU C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 246 Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 632 removed outlier: 6.448A pdb=" N MET A 653 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASN A 707 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 655 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 876 removed outlier: 4.049A pdb=" N TRP A 905 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 902 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 933 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 930 " --> pdb=" O TRP A 960 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N TRP A 962 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 932 " --> pdb=" O TRP A 962 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A1017 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 407 through 408 removed outlier: 6.451A pdb=" N VAL D 282 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 283 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 429 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS D 285 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR D 426 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 317 through 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 709 through 714 removed outlier: 3.663A pdb=" N ASP D 739 " --> pdb=" O LEU D 712 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 785 through 787 removed outlier: 6.625A pdb=" N LEU D 815 " --> pdb=" O ASN D 843 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY D 845 " --> pdb=" O LEU D 815 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 902 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 931 " --> pdb=" O LEU D 901 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 928 " --> pdb=" O CYS D 957 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER D 959 " --> pdb=" O LEU D 928 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU D 930 " --> pdb=" O SER D 959 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET D 986 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D1071 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D1073 " --> pdb=" O LEU D1044 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D1102 " --> pdb=" O LEU D1072 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N VAL D1130 " --> pdb=" O LEU D1099 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU D1101 " --> pdb=" O VAL D1130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1155 through 1156 Processing sheet with id=AB2, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AB3, first strand: chain 'C' and resid 320 through 321 removed outlier: 8.411A pdb=" N ASP C 321 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 282 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 278 " --> pdb=" O GLN C 569 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 567 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE C 282 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA C 565 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS C 547 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 291 through 294 removed outlier: 3.986A pdb=" N ALA C 291 " --> pdb=" O CYS C 304 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 339 through 342 removed outlier: 3.586A pdb=" N THR C 339 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 352 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 361 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 373 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP C 363 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 371 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 382 through 388 removed outlier: 3.630A pdb=" N ALA C 384 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 403 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 416 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 405 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 426 through 430 removed outlier: 3.580A pdb=" N SER C 426 " --> pdb=" O GLY C 437 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 455 " --> pdb=" O CYS C 445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 465 through 468 removed outlier: 4.146A pdb=" N SER C 465 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 498 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 486 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET C 496 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 504 through 509 removed outlier: 3.786A pdb=" N GLY C 520 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE C 524 " --> pdb=" O GLY C 520 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE C 537 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER C 529 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS C 535 " --> pdb=" O SER C 529 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2646 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: 3.71 Time building geometry restraints manager: 2.20 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: 5629 1.34 - 1.45: 2576 1.45 - 1.57: 10156 1.57 - 1.69: 0 1.69 - 1.81: 198 Bond restraints: 18559 Sorted by residual: bond pdb=" CA ILE A 273 " pdb=" CB ILE A 273 " ideal model delta sigma weight residual 1.539 1.522 0.017 5.40e-03 3.43e+04 1.02e+01 bond pdb=" C LEU A 327 " pdb=" O LEU A 327 " ideal model delta sigma weight residual 1.235 1.222 0.013 4.70e-03 4.53e+04 7.75e+00 bond pdb=" N SER D1036 " pdb=" CA SER D1036 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.83e+00 bond pdb=" CA ARG D1033 " pdb=" C ARG D1033 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.38e-02 5.25e+03 4.27e+00 bond pdb=" N LEU D 58 " pdb=" CA LEU D 58 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.75e+00 ... (remaining 18554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 24572 1.63 - 3.26: 464 3.26 - 4.90: 81 4.90 - 6.53: 6 6.53 - 8.16: 2 Bond angle restraints: 25125 Sorted by residual: angle pdb=" N PRO D1035 " pdb=" CA PRO D1035 " pdb=" C PRO D1035 " ideal model delta sigma weight residual 113.53 108.38 5.15 1.39e+00 5.18e-01 1.37e+01 angle pdb=" N ARG D1033 " pdb=" CA ARG D1033 " pdb=" C ARG D1033 " ideal model delta sigma weight residual 113.01 116.51 -3.50 1.20e+00 6.94e-01 8.52e+00 angle pdb=" CB MET D 633 " pdb=" CG MET D 633 " pdb=" SD MET D 633 " ideal model delta sigma weight residual 112.70 120.86 -8.16 3.00e+00 1.11e-01 7.40e+00 angle pdb=" CG MET A 326 " pdb=" SD MET A 326 " pdb=" CE MET A 326 " ideal model delta sigma weight residual 100.90 95.09 5.81 2.20e+00 2.07e-01 6.97e+00 angle pdb=" N GLY A 995 " pdb=" CA GLY A 995 " pdb=" C GLY A 995 " ideal model delta sigma weight residual 113.18 119.12 -5.94 2.37e+00 1.78e-01 6.28e+00 ... (remaining 25120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9891 17.98 - 35.96: 1025 35.96 - 53.94: 229 53.94 - 71.93: 43 71.93 - 89.91: 16 Dihedral angle restraints: 11204 sinusoidal: 4523 harmonic: 6681 Sorted by residual: dihedral pdb=" CA LEU A 994 " pdb=" C LEU A 994 " pdb=" N GLY A 995 " pdb=" CA GLY A 995 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ILE D 743 " pdb=" C ILE D 743 " pdb=" N PHE D 744 " pdb=" CA PHE D 744 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 631 " pdb=" C HIS A 631 " pdb=" N LEU A 632 " pdb=" CA LEU A 632 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 11201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1881 0.030 - 0.060: 661 0.060 - 0.089: 163 0.089 - 0.119: 124 0.119 - 0.149: 21 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CA GLU D1034 " pdb=" N GLU D1034 " pdb=" C GLU D1034 " pdb=" CB GLU D1034 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL C 301 " pdb=" N VAL C 301 " pdb=" C VAL C 301 " pdb=" CB VAL C 301 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE C 282 " pdb=" N ILE C 282 " pdb=" C ILE C 282 " pdb=" CB ILE C 282 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2847 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 543 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO C 544 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 544 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 544 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D1135 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D1136 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D1136 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D1136 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 967 " -0.029 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A 968 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 968 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 968 " -0.024 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 164 2.62 - 3.19: 16153 3.19 - 3.76: 26956 3.76 - 4.33: 36669 4.33 - 4.90: 61462 Nonbonded interactions: 141404 Sorted by model distance: nonbonded pdb=" OH TYR D 315 " pdb=" OE2 GLU D 349 " model vdw 2.046 3.040 nonbonded pdb=" OE2 GLU D 748 " pdb=" NH1 ARG D 796 " model vdw 2.194 3.120 nonbonded pdb=" O LEU D 720 " pdb=" OG SER D 724 " model vdw 2.197 3.040 nonbonded pdb=" O ASP C 410 " pdb=" OD1 ASP C 410 " model vdw 2.198 3.040 nonbonded pdb=" O MET D 760 " pdb=" OG1 THR D 764 " model vdw 2.235 3.040 ... (remaining 141399 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: 8.000 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.790 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 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 : 0.004 0.050 18559 Z= 0.170 Angle : 0.577 8.159 25125 Z= 0.317 Chirality : 0.038 0.149 2850 Planarity : 0.004 0.065 3201 Dihedral : 15.577 89.907 6852 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.05 % Allowed : 11.83 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2276 helix: 1.37 (0.16), residues: 1067 sheet: -0.48 (0.26), residues: 417 loop : -0.79 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 837 TYR 0.015 0.001 TYR A 162 PHE 0.024 0.001 PHE D 243 TRP 0.012 0.001 TRP B 115 HIS 0.007 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00358 (18559) covalent geometry : angle 0.57715 (25125) hydrogen bonds : bond 0.17397 ( 901) hydrogen bonds : angle 6.26946 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: -0.2400 (tpt) cc_final: -0.3649 (ptm) REVERT: A 506 PHE cc_start: 0.5925 (t80) cc_final: 0.5624 (t80) REVERT: D 567 MET cc_start: 0.4101 (mmt) cc_final: 0.3884 (mmm) REVERT: D 1041 ASP cc_start: 0.6955 (t70) cc_final: 0.6454 (t70) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.1535 time to fit residues: 57.7831 Evaluate side-chains 151 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS C 245 GLN C 433 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.159859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.104300 restraints weight = 49974.681| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 5.33 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18559 Z= 0.144 Angle : 0.631 11.042 25125 Z= 0.325 Chirality : 0.042 0.191 2850 Planarity : 0.004 0.053 3201 Dihedral : 4.765 79.044 2469 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.99 % Allowed : 13.82 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2276 helix: 1.59 (0.16), residues: 1082 sheet: -0.04 (0.26), residues: 421 loop : -0.56 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 542 TYR 0.012 0.001 TYR A 241 PHE 0.037 0.002 PHE D 388 TRP 0.021 0.001 TRP A 962 HIS 0.007 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00292 (18559) covalent geometry : angle 0.63124 (25125) hydrogen bonds : bond 0.04630 ( 901) hydrogen bonds : angle 4.88289 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 TRP cc_start: 0.6883 (m100) cc_final: 0.6668 (m100) REVERT: D 1074 ASP cc_start: 0.7693 (t0) cc_final: 0.7474 (t0) REVERT: D 1087 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: D 1140 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7809 (mpp) REVERT: B 93 GLU cc_start: 0.6315 (mp0) cc_final: 0.5290 (mp0) outliers start: 40 outliers final: 22 residues processed: 199 average time/residue: 0.1418 time to fit residues: 43.3081 Evaluate side-chains 166 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A 878 ASN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 728 GLN D 782 HIS D 922 GLN D 979 HIS B 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.101184 restraints weight = 50367.451| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 5.04 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18559 Z= 0.190 Angle : 0.612 11.817 25125 Z= 0.319 Chirality : 0.042 0.178 2850 Planarity : 0.004 0.055 3201 Dihedral : 4.744 82.497 2467 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 14.27 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2276 helix: 1.66 (0.16), residues: 1077 sheet: -0.03 (0.26), residues: 426 loop : -0.66 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 449 TYR 0.016 0.001 TYR C 420 PHE 0.036 0.002 PHE D 388 TRP 0.015 0.001 TRP A 175 HIS 0.006 0.001 HIS D 863 Details of bonding type rmsd covalent geometry : bond 0.00423 (18559) covalent geometry : angle 0.61208 (25125) hydrogen bonds : bond 0.04467 ( 901) hydrogen bonds : angle 4.68523 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5825 (mt-10) REVERT: A 682 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9139 (mp10) REVERT: A 702 MET cc_start: 0.7455 (mmt) cc_final: 0.7089 (mmt) REVERT: A 942 MET cc_start: 0.9146 (tpp) cc_final: 0.8841 (tpp) REVERT: D 540 TRP cc_start: 0.7067 (m100) cc_final: 0.6644 (m100) REVERT: D 1074 ASP cc_start: 0.7722 (t0) cc_final: 0.7492 (t0) REVERT: D 1087 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 1140 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7753 (mpp) REVERT: B 53 TYR cc_start: 0.8091 (m-80) cc_final: 0.7700 (m-80) REVERT: B 55 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: C 258 TRP cc_start: 0.7760 (p90) cc_final: 0.7532 (p90) REVERT: C 477 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8019 (pp) REVERT: C 523 ASP cc_start: 0.7439 (m-30) cc_final: 0.7114 (m-30) outliers start: 50 outliers final: 28 residues processed: 176 average time/residue: 0.1224 time to fit residues: 34.5172 Evaluate side-chains 158 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 571 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 43 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN A 991 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 502 HIS D 675 GLN D 717 ASN ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.154561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.102430 restraints weight = 49682.018| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 5.45 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18559 Z= 0.245 Angle : 0.652 8.642 25125 Z= 0.340 Chirality : 0.044 0.218 2850 Planarity : 0.005 0.053 3201 Dihedral : 4.966 84.979 2467 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.48 % Allowed : 15.37 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2276 helix: 1.56 (0.16), residues: 1083 sheet: -0.20 (0.26), residues: 425 loop : -0.77 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 260 TYR 0.023 0.002 TYR C 420 PHE 0.040 0.002 PHE D 388 TRP 0.019 0.002 TRP A 962 HIS 0.005 0.001 HIS D 863 Details of bonding type rmsd covalent geometry : bond 0.00543 (18559) covalent geometry : angle 0.65186 (25125) hydrogen bonds : bond 0.04582 ( 901) hydrogen bonds : angle 4.73669 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.2099 (OUTLIER) cc_final: 0.1831 (tpp) REVERT: A 702 MET cc_start: 0.7431 (mmt) cc_final: 0.7113 (mmt) REVERT: A 942 MET cc_start: 0.9142 (tpp) cc_final: 0.8868 (tpp) REVERT: D 534 MET cc_start: 0.6243 (ppp) cc_final: 0.6026 (ppp) REVERT: D 540 TRP cc_start: 0.7214 (m100) cc_final: 0.6677 (m100) REVERT: D 709 GLU cc_start: 0.8314 (pm20) cc_final: 0.7900 (mp0) REVERT: D 929 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8646 (mp) REVERT: D 1074 ASP cc_start: 0.7795 (t0) cc_final: 0.7584 (t0) REVERT: D 1087 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: D 1137 LYS cc_start: 0.8875 (tppt) cc_final: 0.8437 (tppt) REVERT: D 1140 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7679 (mpp) REVERT: B 45 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 53 TYR cc_start: 0.8234 (m-80) cc_final: 0.8004 (m-80) REVERT: B 55 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 84 ASP cc_start: 0.8584 (p0) cc_final: 0.7950 (p0) REVERT: B 93 GLU cc_start: 0.6037 (mp0) cc_final: 0.5601 (mp0) REVERT: C 280 MET cc_start: 0.8684 (mtp) cc_final: 0.8331 (mtt) outliers start: 70 outliers final: 40 residues processed: 183 average time/residue: 0.1272 time to fit residues: 36.7857 Evaluate side-chains 172 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 726 CYS Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 571 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 114 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 82 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN D 717 ASN ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.156650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104907 restraints weight = 49604.577| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 5.31 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18559 Z= 0.126 Angle : 0.563 9.857 25125 Z= 0.291 Chirality : 0.041 0.282 2850 Planarity : 0.004 0.066 3201 Dihedral : 4.662 83.665 2467 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.78 % Allowed : 16.66 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2276 helix: 1.74 (0.16), residues: 1082 sheet: -0.01 (0.26), residues: 419 loop : -0.68 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.018 0.001 TYR C 420 PHE 0.039 0.001 PHE D 388 TRP 0.013 0.001 TRP A 175 HIS 0.004 0.001 HIS A 744 Details of bonding type rmsd covalent geometry : bond 0.00272 (18559) covalent geometry : angle 0.56309 (25125) hydrogen bonds : bond 0.03830 ( 901) hydrogen bonds : angle 4.42132 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.3955 (mt) REVERT: A 544 ARG cc_start: 0.6866 (mmt90) cc_final: 0.6571 (mtt90) REVERT: A 584 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5886 (mt-10) REVERT: A 702 MET cc_start: 0.7335 (mmt) cc_final: 0.7106 (mmt) REVERT: A 942 MET cc_start: 0.9119 (tpp) cc_final: 0.8857 (tpp) REVERT: A 1001 MET cc_start: 0.5687 (ttt) cc_final: 0.5399 (tmm) REVERT: D 262 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.5056 (mt-10) REVERT: D 313 PHE cc_start: 0.6764 (p90) cc_final: 0.6461 (p90) REVERT: D 533 ARG cc_start: 0.8548 (ttt90) cc_final: 0.8085 (ttm110) REVERT: D 540 TRP cc_start: 0.7297 (m100) cc_final: 0.6760 (m100) REVERT: D 1074 ASP cc_start: 0.7800 (t0) cc_final: 0.7582 (t0) REVERT: D 1087 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 1137 LYS cc_start: 0.8857 (tppt) cc_final: 0.8430 (tppt) REVERT: D 1140 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7591 (mpp) REVERT: B 45 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: B 53 TYR cc_start: 0.8200 (m-80) cc_final: 0.7595 (m-80) REVERT: C 479 MET cc_start: 0.7445 (mmm) cc_final: 0.7019 (mmm) REVERT: C 523 ASP cc_start: 0.7769 (m-30) cc_final: 0.7230 (m-30) outliers start: 56 outliers final: 33 residues processed: 185 average time/residue: 0.1283 time to fit residues: 37.1575 Evaluate side-chains 169 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 726 CYS Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 571 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 40.0000 chunk 224 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.154849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102677 restraints weight = 49259.647| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 5.09 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18559 Z= 0.183 Angle : 0.588 12.345 25125 Z= 0.304 Chirality : 0.041 0.161 2850 Planarity : 0.004 0.053 3201 Dihedral : 4.668 82.183 2467 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.93 % Allowed : 17.21 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2276 helix: 1.74 (0.16), residues: 1083 sheet: -0.07 (0.26), residues: 429 loop : -0.67 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.019 0.001 TYR C 420 PHE 0.041 0.002 PHE D 388 TRP 0.015 0.001 TRP D 67 HIS 0.005 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00408 (18559) covalent geometry : angle 0.58805 (25125) hydrogen bonds : bond 0.04031 ( 901) hydrogen bonds : angle 4.48738 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.7483 (mmt) cc_final: 0.7270 (mmt) REVERT: A 942 MET cc_start: 0.9150 (tpp) cc_final: 0.8877 (tpp) REVERT: A 1001 MET cc_start: 0.5726 (ttt) cc_final: 0.5519 (tmm) REVERT: D 262 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5016 (mt-10) REVERT: D 540 TRP cc_start: 0.7369 (m100) cc_final: 0.6839 (m100) REVERT: D 1074 ASP cc_start: 0.7771 (t0) cc_final: 0.7558 (t0) REVERT: D 1087 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: D 1137 LYS cc_start: 0.8889 (tppt) cc_final: 0.8453 (tppt) REVERT: D 1140 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7631 (mpp) REVERT: B 45 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: B 53 TYR cc_start: 0.8205 (m-80) cc_final: 0.7579 (m-80) REVERT: B 61 GLU cc_start: 0.8663 (tp30) cc_final: 0.8423 (tp30) REVERT: C 477 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8090 (pp) REVERT: C 523 ASP cc_start: 0.7926 (m-30) cc_final: 0.7452 (m-30) outliers start: 59 outliers final: 39 residues processed: 173 average time/residue: 0.1310 time to fit residues: 35.0608 Evaluate side-chains 172 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 571 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 52 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 216 optimal weight: 0.0770 chunk 82 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS D 983 GLN C 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.157063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100565 restraints weight = 49571.893| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.40 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18559 Z= 0.107 Angle : 0.564 11.183 25125 Z= 0.283 Chirality : 0.040 0.318 2850 Planarity : 0.004 0.048 3201 Dihedral : 4.474 80.985 2467 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 18.35 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2276 helix: 1.80 (0.16), residues: 1085 sheet: 0.04 (0.27), residues: 422 loop : -0.65 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.015 0.001 TYR C 420 PHE 0.041 0.001 PHE D 388 TRP 0.015 0.001 TRP C 446 HIS 0.003 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00225 (18559) covalent geometry : angle 0.56361 (25125) hydrogen bonds : bond 0.03545 ( 901) hydrogen bonds : angle 4.28907 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: -0.0532 (tpp) cc_final: -0.1170 (ptt) REVERT: A 702 MET cc_start: 0.7514 (mmt) cc_final: 0.7280 (mmt) REVERT: A 942 MET cc_start: 0.9114 (tpp) cc_final: 0.8818 (tpp) REVERT: D 262 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5185 (mt-10) REVERT: D 533 ARG cc_start: 0.8485 (ttt90) cc_final: 0.8047 (ttm110) REVERT: D 534 MET cc_start: 0.6455 (ppp) cc_final: 0.6121 (ppp) REVERT: D 540 TRP cc_start: 0.7639 (m100) cc_final: 0.7109 (m100) REVERT: D 1041 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6856 (t70) REVERT: D 1043 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: D 1074 ASP cc_start: 0.7801 (t0) cc_final: 0.7540 (t0) REVERT: D 1087 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: D 1137 LYS cc_start: 0.8827 (tppt) cc_final: 0.8432 (tppt) REVERT: D 1140 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: B 53 TYR cc_start: 0.8144 (m-80) cc_final: 0.7564 (m-80) REVERT: C 422 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.5917 (p0) REVERT: C 479 MET cc_start: 0.7347 (mmm) cc_final: 0.6998 (mmm) REVERT: C 523 ASP cc_start: 0.7829 (m-30) cc_final: 0.7257 (m-30) outliers start: 46 outliers final: 31 residues processed: 185 average time/residue: 0.1319 time to fit residues: 38.2628 Evaluate side-chains 179 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1043 GLU Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 36 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097406 restraints weight = 50063.354| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 5.34 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18559 Z= 0.192 Angle : 0.624 12.727 25125 Z= 0.316 Chirality : 0.042 0.356 2850 Planarity : 0.004 0.053 3201 Dihedral : 4.560 80.662 2467 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.39 % Allowed : 18.80 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2276 helix: 1.72 (0.16), residues: 1091 sheet: -0.07 (0.26), residues: 429 loop : -0.66 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 677 TYR 0.017 0.001 TYR C 420 PHE 0.045 0.002 PHE A1003 TRP 0.017 0.001 TRP C 446 HIS 0.004 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00425 (18559) covalent geometry : angle 0.62417 (25125) hydrogen bonds : bond 0.04005 ( 901) hydrogen bonds : angle 4.45440 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: -0.0523 (tpp) cc_final: -0.1112 (ptt) REVERT: A 702 MET cc_start: 0.7738 (mmt) cc_final: 0.7510 (mmt) REVERT: A 942 MET cc_start: 0.9112 (tpp) cc_final: 0.8811 (tpp) REVERT: D 262 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5246 (mt-10) REVERT: D 533 ARG cc_start: 0.8501 (ttt90) cc_final: 0.8184 (tpp80) REVERT: D 534 MET cc_start: 0.6509 (ppp) cc_final: 0.6153 (ppp) REVERT: D 1074 ASP cc_start: 0.7800 (t0) cc_final: 0.7560 (t0) REVERT: D 1087 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: D 1137 LYS cc_start: 0.8869 (tppt) cc_final: 0.8455 (tppt) REVERT: D 1140 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7598 (mpp) REVERT: B 45 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 53 TYR cc_start: 0.8182 (m-80) cc_final: 0.7508 (m-80) REVERT: C 422 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6084 (p0) REVERT: C 479 MET cc_start: 0.7504 (mmm) cc_final: 0.7121 (mmm) REVERT: C 523 ASP cc_start: 0.7979 (m-30) cc_final: 0.7458 (m-30) outliers start: 48 outliers final: 36 residues processed: 172 average time/residue: 0.1362 time to fit residues: 36.2717 Evaluate side-chains 174 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 201 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 177 optimal weight: 0.0570 chunk 191 optimal weight: 0.8980 chunk 14 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 124 optimal weight: 0.0030 overall best weight: 1.3912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.155724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099537 restraints weight = 49404.727| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.29 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18559 Z= 0.145 Angle : 0.608 10.606 25125 Z= 0.306 Chirality : 0.042 0.324 2850 Planarity : 0.004 0.048 3201 Dihedral : 4.522 80.106 2467 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 19.00 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2276 helix: 1.71 (0.16), residues: 1090 sheet: -0.08 (0.26), residues: 422 loop : -0.66 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.017 0.001 TYR C 420 PHE 0.042 0.001 PHE D 388 TRP 0.015 0.001 TRP C 446 HIS 0.003 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00319 (18559) covalent geometry : angle 0.60792 (25125) hydrogen bonds : bond 0.03804 ( 901) hydrogen bonds : angle 4.41471 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: -0.1048 (tpp) cc_final: -0.1716 (ptt) REVERT: A 683 HIS cc_start: 0.9211 (t70) cc_final: 0.8982 (m170) REVERT: A 702 MET cc_start: 0.7761 (mmt) cc_final: 0.7511 (mmt) REVERT: A 942 MET cc_start: 0.9045 (tpp) cc_final: 0.8747 (tpp) REVERT: D 262 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5215 (mt-10) REVERT: D 533 ARG cc_start: 0.8561 (ttt90) cc_final: 0.8196 (tpp80) REVERT: D 746 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7305 (mmm160) REVERT: D 1041 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7186 (t70) REVERT: D 1043 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: D 1074 ASP cc_start: 0.7834 (t0) cc_final: 0.7571 (t0) REVERT: D 1087 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: D 1137 LYS cc_start: 0.8860 (tppt) cc_final: 0.8463 (tppt) REVERT: D 1140 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7566 (mpp) REVERT: B 45 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 73 MET cc_start: 0.8929 (mtp) cc_final: 0.8683 (mtm) REVERT: C 422 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.5981 (p0) REVERT: C 479 MET cc_start: 0.7453 (mmm) cc_final: 0.7086 (mmm) REVERT: C 523 ASP cc_start: 0.7978 (m-30) cc_final: 0.7367 (m-30) outliers start: 50 outliers final: 36 residues processed: 175 average time/residue: 0.1449 time to fit residues: 39.2901 Evaluate side-chains 175 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1043 GLU Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.0770 chunk 211 optimal weight: 0.9990 chunk 30 optimal weight: 40.0000 chunk 202 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 188 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 chunk 28 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 729 HIS ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.157396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101234 restraints weight = 49891.223| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.95 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18559 Z= 0.108 Angle : 0.598 10.672 25125 Z= 0.297 Chirality : 0.041 0.309 2850 Planarity : 0.004 0.048 3201 Dihedral : 4.378 78.502 2467 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 19.09 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2276 helix: 1.73 (0.16), residues: 1095 sheet: 0.01 (0.26), residues: 422 loop : -0.59 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.030 0.001 TYR C 432 PHE 0.043 0.001 PHE D 388 TRP 0.017 0.001 TRP C 446 HIS 0.003 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00234 (18559) covalent geometry : angle 0.59833 (25125) hydrogen bonds : bond 0.03472 ( 901) hydrogen bonds : angle 4.32286 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.7670 (mmt) cc_final: 0.7423 (mmt) REVERT: A 942 MET cc_start: 0.9064 (tpp) cc_final: 0.8768 (tpp) REVERT: D 262 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5209 (mt-10) REVERT: D 746 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7231 (mmm160) REVERT: D 856 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8379 (mpp) REVERT: D 999 PHE cc_start: 0.8065 (m-80) cc_final: 0.7837 (m-10) REVERT: D 1041 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7074 (t70) REVERT: D 1043 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: D 1074 ASP cc_start: 0.7861 (t0) cc_final: 0.7590 (t0) REVERT: D 1087 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: D 1137 LYS cc_start: 0.8847 (tppt) cc_final: 0.8458 (tppt) REVERT: D 1140 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7548 (mpp) REVERT: B 45 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 53 TYR cc_start: 0.8082 (m-80) cc_final: 0.7718 (m-80) REVERT: C 422 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5870 (p0) REVERT: C 479 MET cc_start: 0.7343 (mmm) cc_final: 0.7022 (mmm) REVERT: C 523 ASP cc_start: 0.7918 (m-30) cc_final: 0.7340 (m-30) outliers start: 47 outliers final: 32 residues processed: 174 average time/residue: 0.1403 time to fit residues: 38.2125 Evaluate side-chains 170 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 856 MET Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1042 LEU Chi-restraints excluded: chain D residue 1043 GLU Chi-restraints excluded: chain D residue 1072 LEU Chi-restraints excluded: chain D residue 1087 GLU Chi-restraints excluded: chain D residue 1108 SER Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 13 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098208 restraints weight = 49415.725| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 5.54 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18559 Z= 0.179 Angle : 0.630 11.832 25125 Z= 0.317 Chirality : 0.043 0.396 2850 Planarity : 0.004 0.048 3201 Dihedral : 4.481 78.012 2467 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 18.95 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2276 helix: 1.75 (0.16), residues: 1092 sheet: -0.04 (0.26), residues: 427 loop : -0.65 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.019 0.001 TYR C 420 PHE 0.041 0.002 PHE D 388 TRP 0.013 0.001 TRP D 67 HIS 0.007 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00395 (18559) covalent geometry : angle 0.63023 (25125) hydrogen bonds : bond 0.03884 ( 901) hydrogen bonds : angle 4.43876 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.76 seconds wall clock time: 91 minutes 29.09 seconds (5489.09 seconds total)