Starting phenix.real_space_refine on Fri Jun 13 21:36:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.map" model { file = "/net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ep4_19872/06_2025/9ep4_19872.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 85 5.16 5 C 9832 2.51 5 N 2691 2.21 5 O 2785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15393 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 884, 6542 Classifications: {'peptide': 884} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 31, 'TRANS': 852} Chain breaks: 10 Unresolved non-hydrogen bonds: 584 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 330 Chain: "B" Number of atoms: 5945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 5945 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 755} Chain breaks: 9 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2906 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 14.47, per 1000 atoms: 0.94 Number of scatterers: 15393 At special positions: 0 Unit cell: (93.48, 116.44, 253.38, 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 85 16.00 O 2785 8.00 N 2691 7.00 C 9832 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: 4.20 Conformation dependent library (CDL) restraints added in 2.2 seconds 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3938 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 1 sheets defined 81.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.746A pdb=" N GLU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.732A pdb=" N LYS A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.505A pdb=" N LEU A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 127 through 131 removed outlier: 4.107A pdb=" N ASP A 131 " --> pdb=" O HIS A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 136 through 159 removed outlier: 4.043A pdb=" N SER A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.534A pdb=" N SER A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 264 Processing helix chain 'A' and resid 267 through 289 removed outlier: 4.208A pdb=" N TYR A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.612A pdb=" N VAL A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 removed outlier: 3.786A pdb=" N GLN A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 395 removed outlier: 4.226A pdb=" N ILE A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.269A pdb=" N ASN A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.895A pdb=" N LEU A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.629A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.994A pdb=" N LEU A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.713A pdb=" N LEU A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 551 through 559 removed outlier: 4.056A pdb=" N GLY A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 583 Processing helix chain 'A' and resid 585 through 601 removed outlier: 3.578A pdb=" N ALA A 589 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 626 Processing helix chain 'A' and resid 636 through 647 Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.695A pdb=" N ALA A 660 " --> pdb=" O ARG A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 4.013A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 688 removed outlier: 3.885A pdb=" N LEU A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 Processing helix chain 'A' and resid 710 through 725 removed outlier: 4.327A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 766 through 783 removed outlier: 3.607A pdb=" N VAL A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 829 Processing helix chain 'A' and resid 832 through 846 removed outlier: 3.513A pdb=" N THR A 846 " --> pdb=" O ILE A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 864 Processing helix chain 'A' and resid 877 through 891 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.858A pdb=" N GLN A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 removed outlier: 3.615A pdb=" N ALA A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 932 removed outlier: 4.147A pdb=" N ASP A 930 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 949 Processing helix chain 'A' and resid 950 through 962 Processing helix chain 'A' and resid 973 through 995 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 94 removed outlier: 3.829A pdb=" N GLU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 136 through 158 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 183 through 201 Processing helix chain 'B' and resid 205 through 220 removed outlier: 4.102A pdb=" N GLN B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 234 removed outlier: 4.226A pdb=" N VAL B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 253 removed outlier: 3.705A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 321 removed outlier: 4.019A pdb=" N SER B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.593A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 380 through 398 Processing helix chain 'B' and resid 402 through 413 Processing helix chain 'B' and resid 429 through 451 Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.670A pdb=" N TRP B 498 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 526 Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.757A pdb=" N ALA B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 562 removed outlier: 3.868A pdb=" N LEU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 587 Processing helix chain 'B' and resid 590 through 596 Processing helix chain 'B' and resid 598 through 605 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 618 through 632 removed outlier: 3.742A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 663 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 679 Processing helix chain 'B' and resid 681 through 698 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.886A pdb=" N GLY B 706 " --> pdb=" O GLU B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 788 removed outlier: 3.696A pdb=" N VAL B 772 " --> pdb=" O ASN B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 821 removed outlier: 3.847A pdb=" N ALA B 809 " --> pdb=" O SER B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 839 removed outlier: 3.541A pdb=" N ARG B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 854 Processing helix chain 'B' and resid 855 through 867 removed outlier: 3.646A pdb=" N GLU B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 removed outlier: 4.172A pdb=" N LEU B 871 " --> pdb=" O PRO B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 892 Processing helix chain 'B' and resid 900 through 917 Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 927 through 934 removed outlier: 4.326A pdb=" N SER B 932 " --> pdb=" O GLU B 929 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 934 " --> pdb=" O PHE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 953 Processing helix chain 'B' and resid 956 through 958 No H-bonds generated for 'chain 'B' and resid 956 through 958' Processing helix chain 'B' and resid 972 through 977 removed outlier: 3.896A pdb=" N GLU B 976 " --> pdb=" O ASP B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 995 removed outlier: 3.964A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 988 " --> pdb=" O HIS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1000 Processing helix chain 'B' and resid 1001 through 1006 removed outlier: 3.555A pdb=" N GLY B1004 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B1006 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 removed outlier: 3.671A pdb=" N ARG D 10 " --> pdb=" O HIS D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 35 Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.769A pdb=" N VAL D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 85 Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.094A pdb=" N SER D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 140 Processing helix chain 'D' and resid 141 through 158 removed outlier: 3.561A pdb=" N CYS D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.695A pdb=" N LEU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.980A pdb=" N ILE D 197 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 213 Processing helix chain 'D' and resid 214 through 217 removed outlier: 3.651A pdb=" N ILE D 217 " --> pdb=" O PRO D 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 214 through 217' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 239 through 257 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 277 through 308 removed outlier: 3.931A pdb=" N GLN D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 Proline residue: D 324 - end of helix Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 341 through 362 Processing helix chain 'D' and resid 368 through 376 Processing helix chain 'D' and resid 377 through 379 No H-bonds generated for 'chain 'D' and resid 377 through 379' Processing helix chain 'D' and resid 382 through 390 Processing sheet with id=AA1, first strand: chain 'B' and resid 960 through 963 1124 hydrogen bonds defined for protein. 3321 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: 5.29 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2526 1.30 - 1.43: 3841 1.43 - 1.56: 9209 1.56 - 1.69: 1 1.69 - 1.83: 114 Bond restraints: 15691 Sorted by residual: bond pdb=" C SER B 658 " pdb=" O SER B 658 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.15e-02 7.56e+03 3.89e+01 bond pdb=" C LEU B 878 " pdb=" O LEU B 878 " ideal model delta sigma weight residual 1.236 1.164 0.073 1.24e-02 6.50e+03 3.43e+01 bond pdb=" C ALA B 912 " pdb=" O ALA B 912 " ideal model delta sigma weight residual 1.236 1.170 0.067 1.15e-02 7.56e+03 3.36e+01 bond pdb=" C HIS B 662 " pdb=" O HIS B 662 " ideal model delta sigma weight residual 1.235 1.295 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" C LEU B 885 " pdb=" O LEU B 885 " ideal model delta sigma weight residual 1.237 1.281 -0.044 1.16e-02 7.43e+03 1.45e+01 ... (remaining 15686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 20621 2.07 - 4.14: 611 4.14 - 6.21: 94 6.21 - 8.28: 23 8.28 - 10.35: 8 Bond angle restraints: 21357 Sorted by residual: angle pdb=" N VAL A 456 " pdb=" CA VAL A 456 " pdb=" C VAL A 456 " ideal model delta sigma weight residual 110.62 102.24 8.38 1.02e+00 9.61e-01 6.75e+01 angle pdb=" C HIS B 451 " pdb=" CA HIS B 451 " pdb=" CB HIS B 451 " ideal model delta sigma weight residual 111.76 102.13 9.63 1.47e+00 4.63e-01 4.29e+01 angle pdb=" CA SER B 658 " pdb=" C SER B 658 " pdb=" O SER B 658 " ideal model delta sigma weight residual 120.90 114.09 6.81 1.07e+00 8.73e-01 4.05e+01 angle pdb=" N ALA B 884 " pdb=" CA ALA B 884 " pdb=" C ALA B 884 " ideal model delta sigma weight residual 111.36 105.14 6.22 1.09e+00 8.42e-01 3.26e+01 angle pdb=" N SER B 658 " pdb=" CA SER B 658 " pdb=" C SER B 658 " ideal model delta sigma weight residual 111.11 104.34 6.77 1.20e+00 6.94e-01 3.18e+01 ... (remaining 21352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8464 17.52 - 35.03: 796 35.03 - 52.55: 179 52.55 - 70.07: 30 70.07 - 87.59: 12 Dihedral angle restraints: 9481 sinusoidal: 3460 harmonic: 6021 Sorted by residual: dihedral pdb=" CA LEU A 468 " pdb=" C LEU A 468 " pdb=" N LEU A 469 " pdb=" CA LEU A 469 " ideal model delta harmonic sigma weight residual 180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TRP A 670 " pdb=" C TRP A 670 " pdb=" N ARG A 671 " pdb=" CA ARG A 671 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE B 223 " pdb=" C PHE B 223 " pdb=" N ASP B 224 " pdb=" CA ASP B 224 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2263 0.068 - 0.137: 254 0.137 - 0.205: 22 0.205 - 0.274: 11 0.274 - 0.342: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CB VAL B 392 " pdb=" CA VAL B 392 " pdb=" CG1 VAL B 392 " pdb=" CG2 VAL B 392 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA HIS B 662 " pdb=" N HIS B 662 " pdb=" C HIS B 662 " pdb=" CB HIS B 662 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA HIS B 451 " pdb=" N HIS B 451 " pdb=" C HIS B 451 " pdb=" CB HIS B 451 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2548 not shown) Planarity restraints: 2729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 970 " -0.101 5.00e-02 4.00e+02 1.49e-01 3.56e+01 pdb=" N PRO A 971 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO A 971 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 971 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 704 " -0.055 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 705 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 706 " -0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO A 707 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 707 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 707 " -0.044 5.00e-02 4.00e+02 ... (remaining 2726 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2093 2.75 - 3.29: 16312 3.29 - 3.82: 26364 3.82 - 4.36: 29702 4.36 - 4.90: 50313 Nonbonded interactions: 124784 Sorted by model distance: nonbonded pdb=" O CYS B 872 " pdb=" OG SER B 875 " model vdw 2.212 3.040 nonbonded pdb=" O SER D 119 " pdb=" OH TYR D 156 " model vdw 2.216 3.040 nonbonded pdb=" O SER B 819 " pdb=" NH1 ARG B 850 " model vdw 2.227 3.120 nonbonded pdb=" O TRP D 136 " pdb=" OG1 THR D 140 " model vdw 2.237 3.040 nonbonded pdb=" O LYS B 36 " pdb=" OG1 THR B 40 " model vdw 2.270 3.040 ... (remaining 124779 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: 342.920 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.850 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 390.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 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 : 0.005 0.088 15691 Z= 0.285 Angle : 0.830 10.348 21357 Z= 0.505 Chirality : 0.047 0.342 2551 Planarity : 0.007 0.149 2729 Dihedral : 14.857 87.586 5543 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 0.51 % Allowed : 13.67 % Favored : 85.82 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2018 helix: 0.93 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 225 HIS 0.010 0.001 HIS A 579 PHE 0.038 0.003 PHE A 345 TYR 0.028 0.003 TYR A 326 ARG 0.007 0.001 ARG B 998 Details of bonding type rmsd hydrogen bonds : bond 0.15382 ( 1124) hydrogen bonds : angle 6.12719 ( 3321) covalent geometry : bond 0.00525 (15691) covalent geometry : angle 0.82989 (21357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.899 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 116 LEU cc_start: 0.6750 (tp) cc_final: 0.6536 (pp) REVERT: A 752 MET cc_start: 0.2764 (ttt) cc_final: 0.2240 (ttt) REVERT: B 879 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6949 (ptp90) REVERT: D 111 MET cc_start: 0.0026 (tpt) cc_final: -0.0341 (mmp) outliers start: 8 outliers final: 3 residues processed: 136 average time/residue: 0.2740 time to fit residues: 56.6605 Evaluate side-chains 115 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 879 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS ** A 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 643 GLN B 775 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.242946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.203885 restraints weight = 26815.225| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 3.02 r_work: 0.4363 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15691 Z= 0.155 Angle : 0.611 13.440 21357 Z= 0.312 Chirality : 0.039 0.206 2551 Planarity : 0.005 0.106 2729 Dihedral : 4.669 47.501 2186 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.23 % Allowed : 13.41 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2018 helix: 1.56 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 225 HIS 0.007 0.001 HIS A 579 PHE 0.021 0.002 PHE A 995 TYR 0.018 0.002 TYR B 774 ARG 0.009 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1124) hydrogen bonds : angle 4.37307 ( 3321) covalent geometry : bond 0.00338 (15691) covalent geometry : angle 0.61095 (21357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 PHE cc_start: 0.6026 (t80) cc_final: 0.4145 (t80) REVERT: A 752 MET cc_start: 0.3490 (ttt) cc_final: 0.2813 (ttt) REVERT: A 896 GLN cc_start: 0.4489 (mt0) cc_final: 0.4180 (mm-40) REVERT: B 193 TYR cc_start: 0.8195 (t80) cc_final: 0.7977 (t80) REVERT: B 393 HIS cc_start: 0.4465 (OUTLIER) cc_final: 0.4263 (m-70) REVERT: B 879 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: D 111 MET cc_start: -0.0362 (tpt) cc_final: -0.0763 (mmp) outliers start: 35 outliers final: 9 residues processed: 147 average time/residue: 0.2477 time to fit residues: 57.7496 Evaluate side-chains 121 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 899 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 171 optimal weight: 0.0470 chunk 66 optimal weight: 0.5980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 262 GLN A 579 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 662 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.239174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.197776 restraints weight = 26307.452| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 2.81 r_work: 0.4306 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15691 Z= 0.199 Angle : 0.645 14.112 21357 Z= 0.324 Chirality : 0.041 0.269 2551 Planarity : 0.005 0.079 2729 Dihedral : 4.464 45.852 2180 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 13.48 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2018 helix: 1.55 (0.13), residues: 1550 sheet: None (None), residues: 0 loop : -0.24 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 225 HIS 0.012 0.001 HIS A 579 PHE 0.024 0.002 PHE A 995 TYR 0.020 0.002 TYR B 539 ARG 0.007 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 1124) hydrogen bonds : angle 4.38477 ( 3321) covalent geometry : bond 0.00447 (15691) covalent geometry : angle 0.64499 (21357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.8296 (tt0) cc_final: 0.8087 (tt0) REVERT: A 337 ASN cc_start: 0.4822 (t0) cc_final: 0.4203 (t0) REVERT: A 403 PHE cc_start: 0.6128 (t80) cc_final: 0.4065 (t80) REVERT: A 752 MET cc_start: 0.3917 (ttt) cc_final: 0.3440 (ttt) REVERT: A 780 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7271 (tt) REVERT: A 938 LEU cc_start: 0.6703 (mt) cc_final: 0.6424 (tp) REVERT: B 193 TYR cc_start: 0.8307 (t80) cc_final: 0.8054 (t80) REVERT: B 225 TRP cc_start: 0.7293 (p-90) cc_final: 0.6969 (p-90) REVERT: B 393 HIS cc_start: 0.4482 (OUTLIER) cc_final: 0.3025 (m-70) REVERT: B 879 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7034 (ttm170) REVERT: B 996 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.5900 (mm) REVERT: D 111 MET cc_start: 0.0076 (tpt) cc_final: -0.0537 (mmp) REVERT: D 200 MET cc_start: 0.5290 (mtt) cc_final: 0.5040 (mtt) outliers start: 44 outliers final: 21 residues processed: 159 average time/residue: 0.2503 time to fit residues: 62.5253 Evaluate side-chains 146 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 132 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 178 optimal weight: 0.0470 chunk 146 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN B 836 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.240870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.200751 restraints weight = 26588.823| |-----------------------------------------------------------------------------| r_work (start): 0.4705 rms_B_bonded: 2.88 r_work: 0.4343 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15691 Z= 0.139 Angle : 0.573 14.739 21357 Z= 0.286 Chirality : 0.038 0.156 2551 Planarity : 0.005 0.072 2729 Dihedral : 4.193 32.945 2180 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.61 % Allowed : 15.51 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2018 helix: 1.80 (0.13), residues: 1555 sheet: None (None), residues: 0 loop : -0.24 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 225 HIS 0.012 0.001 HIS B 393 PHE 0.019 0.002 PHE A 777 TYR 0.021 0.002 TYR A 855 ARG 0.007 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1124) hydrogen bonds : angle 4.09056 ( 3321) covalent geometry : bond 0.00313 (15691) covalent geometry : angle 0.57280 (21357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.8157 (tt0) cc_final: 0.7948 (tt0) REVERT: A 403 PHE cc_start: 0.6007 (t80) cc_final: 0.4092 (t80) REVERT: A 752 MET cc_start: 0.3768 (ttt) cc_final: 0.3334 (ttt) REVERT: A 772 ILE cc_start: 0.6307 (mm) cc_final: 0.6046 (tt) REVERT: A 780 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7204 (tt) REVERT: B 181 MET cc_start: 0.6951 (mmp) cc_final: 0.5941 (mmp) REVERT: B 193 TYR cc_start: 0.8309 (t80) cc_final: 0.8033 (t80) REVERT: B 225 TRP cc_start: 0.7143 (p-90) cc_final: 0.6825 (p-90) REVERT: B 317 PHE cc_start: 0.4664 (t80) cc_final: 0.4006 (t80) REVERT: B 393 HIS cc_start: 0.4374 (OUTLIER) cc_final: 0.4151 (t70) REVERT: B 996 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.5586 (mm) REVERT: D 111 MET cc_start: 0.0159 (tpt) cc_final: -0.0486 (mmp) REVERT: D 200 MET cc_start: 0.5418 (mtt) cc_final: 0.5170 (mtt) outliers start: 41 outliers final: 24 residues processed: 160 average time/residue: 0.2383 time to fit residues: 61.0603 Evaluate side-chains 155 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 855 TYR Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain D residue 221 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 92 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 836 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.239979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.200854 restraints weight = 26799.319| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 2.66 r_work: 0.4349 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15691 Z= 0.149 Angle : 0.584 14.630 21357 Z= 0.290 Chirality : 0.039 0.241 2551 Planarity : 0.005 0.073 2729 Dihedral : 4.067 21.303 2176 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.12 % Allowed : 15.45 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2018 helix: 1.89 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.23 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 225 HIS 0.006 0.001 HIS B 219 PHE 0.019 0.002 PHE A 777 TYR 0.020 0.002 TYR A 855 ARG 0.004 0.000 ARG B 971 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 1124) hydrogen bonds : angle 4.06910 ( 3321) covalent geometry : bond 0.00341 (15691) covalent geometry : angle 0.58444 (21357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 1.917 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 403 PHE cc_start: 0.6021 (t80) cc_final: 0.4191 (t80) REVERT: A 752 MET cc_start: 0.3591 (ttt) cc_final: 0.3260 (ttt) REVERT: A 842 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5202 (tt) REVERT: A 929 TYR cc_start: 0.4850 (m-10) cc_final: 0.3925 (m-10) REVERT: A 938 LEU cc_start: 0.6745 (mt) cc_final: 0.6470 (tp) REVERT: B 317 PHE cc_start: 0.4788 (t80) cc_final: 0.4101 (t80) REVERT: B 347 MET cc_start: 0.3734 (mmp) cc_final: 0.3218 (mmm) REVERT: B 393 HIS cc_start: 0.4874 (OUTLIER) cc_final: 0.4602 (m-70) REVERT: D 111 MET cc_start: -0.0274 (tpt) cc_final: -0.0889 (mmp) REVERT: D 200 MET cc_start: 0.5322 (mtt) cc_final: 0.5032 (mtt) outliers start: 49 outliers final: 30 residues processed: 181 average time/residue: 0.2672 time to fit residues: 74.5224 Evaluate side-chains 156 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 987 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 126 optimal weight: 0.0070 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.0270 chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS B 770 GLN B 836 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.241004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.201061 restraints weight = 26647.148| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 2.63 r_work: 0.4358 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15691 Z= 0.132 Angle : 0.572 15.033 21357 Z= 0.284 Chirality : 0.038 0.191 2551 Planarity : 0.005 0.073 2729 Dihedral : 3.957 21.121 2176 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.05 % Allowed : 15.89 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 2018 helix: 2.01 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 225 HIS 0.006 0.001 HIS B 219 PHE 0.015 0.001 PHE A 995 TYR 0.013 0.001 TYR B 774 ARG 0.006 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1124) hydrogen bonds : angle 3.98795 ( 3321) covalent geometry : bond 0.00301 (15691) covalent geometry : angle 0.57186 (21357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.609 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 151 ILE cc_start: 0.4431 (OUTLIER) cc_final: 0.4083 (tp) REVERT: A 403 PHE cc_start: 0.6007 (t80) cc_final: 0.4216 (t80) REVERT: A 509 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.3865 (tt) REVERT: A 752 MET cc_start: 0.3452 (ttt) cc_final: 0.3127 (ttt) REVERT: A 876 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: A 938 LEU cc_start: 0.6771 (mt) cc_final: 0.6505 (tp) REVERT: B 317 PHE cc_start: 0.4649 (t80) cc_final: 0.3926 (t80) REVERT: B 996 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6036 (mm) REVERT: D 111 MET cc_start: -0.0194 (tpt) cc_final: -0.0857 (mmp) REVERT: D 200 MET cc_start: 0.5375 (mtt) cc_final: 0.5106 (mtt) outliers start: 48 outliers final: 30 residues processed: 162 average time/residue: 0.2377 time to fit residues: 61.0162 Evaluate side-chains 162 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 91 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.236611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.197474 restraints weight = 26658.865| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.55 r_work: 0.4242 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15691 Z= 0.214 Angle : 0.674 14.848 21357 Z= 0.334 Chirality : 0.042 0.294 2551 Planarity : 0.005 0.072 2729 Dihedral : 4.274 22.900 2176 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.12 % Allowed : 16.02 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2018 helix: 1.64 (0.13), residues: 1569 sheet: None (None), residues: 0 loop : -0.26 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 225 HIS 0.008 0.001 HIS B 598 PHE 0.029 0.002 PHE A 777 TYR 0.018 0.002 TYR B 539 ARG 0.005 0.000 ARG A 754 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1124) hydrogen bonds : angle 4.34711 ( 3321) covalent geometry : bond 0.00494 (15691) covalent geometry : angle 0.67391 (21357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 1.801 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: A 151 ILE cc_start: 0.4224 (OUTLIER) cc_final: 0.3936 (tp) REVERT: A 403 PHE cc_start: 0.6370 (t80) cc_final: 0.4417 (t80) REVERT: A 697 LEU cc_start: -0.0493 (OUTLIER) cc_final: -0.1395 (tt) REVERT: A 752 MET cc_start: 0.4120 (ttt) cc_final: 0.3666 (ttt) REVERT: B 347 MET cc_start: 0.3943 (mmp) cc_final: 0.3441 (mmm) REVERT: B 996 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6579 (mm) REVERT: D 111 MET cc_start: 0.0565 (tpt) cc_final: -0.0303 (mmp) REVERT: D 200 MET cc_start: 0.5497 (mtt) cc_final: 0.5286 (mtt) outliers start: 49 outliers final: 38 residues processed: 161 average time/residue: 0.2426 time to fit residues: 61.5464 Evaluate side-chains 165 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 527 ARG Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 54 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 137 optimal weight: 0.0870 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.239626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.201212 restraints weight = 26289.611| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 2.77 r_work: 0.4349 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15691 Z= 0.125 Angle : 0.583 15.488 21357 Z= 0.285 Chirality : 0.037 0.171 2551 Planarity : 0.005 0.074 2729 Dihedral : 3.962 21.287 2176 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.97 % Allowed : 17.29 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2018 helix: 2.01 (0.13), residues: 1555 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 225 HIS 0.006 0.001 HIS A 514 PHE 0.014 0.001 PHE B 379 TYR 0.013 0.001 TYR A 994 ARG 0.005 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 1124) hydrogen bonds : angle 3.95235 ( 3321) covalent geometry : bond 0.00282 (15691) covalent geometry : angle 0.58342 (21357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.701 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: A 151 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3783 (tp) REVERT: A 403 PHE cc_start: 0.6023 (t80) cc_final: 0.4202 (t80) REVERT: A 697 LEU cc_start: -0.0704 (OUTLIER) cc_final: -0.1560 (tt) REVERT: A 752 MET cc_start: 0.3632 (ttt) cc_final: 0.3269 (ttt) REVERT: B 181 MET cc_start: 0.7543 (tpp) cc_final: 0.7334 (mtm) REVERT: B 347 MET cc_start: 0.3964 (mmp) cc_final: 0.3469 (mmm) REVERT: B 996 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6135 (mm) REVERT: D 111 MET cc_start: 0.0298 (tpt) cc_final: -0.0528 (mmp) REVERT: D 200 MET cc_start: 0.5482 (mtt) cc_final: 0.5255 (mtt) outliers start: 31 outliers final: 23 residues processed: 152 average time/residue: 0.2464 time to fit residues: 58.3437 Evaluate side-chains 148 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.237940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.198437 restraints weight = 26081.107| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 2.85 r_work: 0.4316 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15691 Z= 0.152 Angle : 0.631 15.179 21357 Z= 0.306 Chirality : 0.040 0.327 2551 Planarity : 0.005 0.074 2729 Dihedral : 4.043 23.422 2176 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 18.05 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 2018 helix: 1.99 (0.13), residues: 1554 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 225 HIS 0.006 0.001 HIS A 514 PHE 0.020 0.002 PHE A 777 TYR 0.015 0.002 TYR A 855 ARG 0.009 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 1124) hydrogen bonds : angle 4.07655 ( 3321) covalent geometry : bond 0.00352 (15691) covalent geometry : angle 0.63085 (21357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.802 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: A 151 ILE cc_start: 0.4061 (OUTLIER) cc_final: 0.3771 (tp) REVERT: A 403 PHE cc_start: 0.6112 (t80) cc_final: 0.4280 (t80) REVERT: A 535 MET cc_start: 0.4688 (ptm) cc_final: 0.4418 (ptm) REVERT: A 752 MET cc_start: 0.3731 (ttt) cc_final: 0.3396 (ttt) REVERT: A 973 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5836 (pm20) REVERT: B 181 MET cc_start: 0.7746 (tpp) cc_final: 0.7341 (mmp) REVERT: B 347 MET cc_start: 0.4011 (mmp) cc_final: 0.3552 (mmm) REVERT: B 996 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6182 (mm) REVERT: D 111 MET cc_start: 0.0333 (tpt) cc_final: -0.0527 (mmp) REVERT: D 200 MET cc_start: 0.5521 (mtt) cc_final: 0.5305 (mtt) outliers start: 32 outliers final: 25 residues processed: 148 average time/residue: 0.2456 time to fit residues: 57.3367 Evaluate side-chains 148 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 142 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 146 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.238238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.199910 restraints weight = 26258.434| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 2.89 r_work: 0.4323 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15691 Z= 0.139 Angle : 0.612 15.251 21357 Z= 0.299 Chirality : 0.039 0.262 2551 Planarity : 0.005 0.074 2729 Dihedral : 3.960 20.480 2176 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.84 % Allowed : 18.12 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 2018 helix: 2.04 (0.13), residues: 1553 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 225 HIS 0.006 0.001 HIS A 514 PHE 0.016 0.002 PHE A 995 TYR 0.015 0.001 TYR B 774 ARG 0.006 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 1124) hydrogen bonds : angle 4.01197 ( 3321) covalent geometry : bond 0.00319 (15691) covalent geometry : angle 0.61238 (21357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.663 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: A 151 ILE cc_start: 0.4103 (OUTLIER) cc_final: 0.3796 (tp) REVERT: A 403 PHE cc_start: 0.6066 (t80) cc_final: 0.4280 (t80) REVERT: A 458 MET cc_start: 0.5377 (ttm) cc_final: 0.5159 (mtp) REVERT: A 752 MET cc_start: 0.3733 (ttt) cc_final: 0.3397 (ttt) REVERT: A 973 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5820 (pm20) REVERT: B 181 MET cc_start: 0.7771 (tpp) cc_final: 0.7355 (mtp) REVERT: B 347 MET cc_start: 0.4040 (mmp) cc_final: 0.3663 (mmm) REVERT: B 996 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6070 (mm) REVERT: D 111 MET cc_start: 0.0053 (tpt) cc_final: -0.0751 (mmp) REVERT: D 200 MET cc_start: 0.5517 (mtt) cc_final: 0.5289 (mtt) outliers start: 29 outliers final: 25 residues processed: 153 average time/residue: 0.2481 time to fit residues: 59.4082 Evaluate side-chains 153 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 899 HIS Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 996 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 132 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 161 optimal weight: 0.0670 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.237497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.197557 restraints weight = 25889.872| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 3.08 r_work: 0.4299 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15691 Z= 0.151 Angle : 0.627 14.804 21357 Z= 0.307 Chirality : 0.039 0.236 2551 Planarity : 0.005 0.073 2729 Dihedral : 3.996 20.993 2176 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.03 % Allowed : 18.18 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 2018 helix: 1.96 (0.13), residues: 1561 sheet: None (None), residues: 0 loop : -0.19 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 225 HIS 0.007 0.001 HIS B 219 PHE 0.019 0.002 PHE A 777 TYR 0.018 0.002 TYR B 774 ARG 0.006 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 1124) hydrogen bonds : angle 4.07475 ( 3321) covalent geometry : bond 0.00347 (15691) covalent geometry : angle 0.62734 (21357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12686.17 seconds wall clock time: 220 minutes 52.99 seconds (13252.99 seconds total)